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Large-scale studies

Data Summary

Published Variant
- SNP: 1391
- CNV: 398
- Others: 173
Published Gene: 359
Published Region: 128
Pathway by PBA: 8
Study: 361

Detail ...

SNP Report

Basic Info

Name	rs2439832 dbSNP Ensembl
Location	Chr15:43779686(Fwd)
Variant Alleles	C/T
Ancestral Allele	T
Functional Annotation	intron_variant; nc_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000263801; ENST00000572085; ENST00000450115; ENST00000413546; ENST00000382039; ENST00000382044) nc_transcript_variant(ENST00000572085)
No. of Studies	2 (significant: 0; non-significant: 2; trend: 0)
Source	Literature-origin

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result of Statistical Analysis
Lantieri F, 2010	T:C		Binomial P-value=0.68, OR=1.06 for whole sample; Binomial P-...... Binomial P-value=0.68, OR=1.06 for whole sample; Binomial P-value=0.46, OR=0.96 for C-subtype More...	no significant association no significant association	Non-significant
Neale BM, 2008	T:C		Uncorrected TDT P-value=4.66E-05 (OR=0.6567) Uncorrected TDT P-value=4.66E-05 (OR=0.6567)	One of top 25 results in uncorrected TDT test One of top 25 results in uncorrected TDT test	Non-significant

SNP related genes (count: 1)

Literature-origin genes (count: 0)

Genes from other sources (count: 1)

Approved Symbol	Approved Name	Location
TP53BP1	tumor protein p53 binding protein 1	15q15-q21

SNPs in LD with rs2439832 (count: 120) View in gBrowse (chr15:43594900..43939642 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²>=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 120)

rs_ID	Functional Annotation	r²[population]
rs1869258	intron_variant; upstream_gene_variant	0.954[CHB]; 0.878[CHD]; 1.0[JPT]
rs2255410	intron_variant	0.953[JPT]
rs2602141	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; intron_variant; missense_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs2264876	intron_variant; nc_transcript_variant	1.0[ASW]; 0.953[CHB]; 0.926[CHD]; 1.0[GIH]; 0.952[JPT]; 1.0[LWK]; 0.897[MEX]; 0.865[MKK]; 0.918[TSI]; 1.0[YRI]
rs7181634	3_prime_UTR_variant; downstream_gene_variant; intron_variant	0.942[YRI]
rs2255663	intron_variant	0.953[JPT]
rs690436	intron_variant; nc_transcript_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 1.0[MEX]; 0.959[TSI]
rs12913977	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[YRI]
rs10518812	3_prime_UTR_variant; downstream_gene_variant	0.942[YRI]
rs16957715	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.801[LWK]; 1.0[YRI]
rs2467745	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs690316	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.872[ASW]; 0.848[CEU]; 0.954[CHB]; 0.926[CHD]; 0.953[JPT]; 0.974[LWK]; 0.896[MEX]; 0.866[MKK]; 0.959[TSI]; 1.0[YRI]
rs12914122	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[YRI]
rs2614811	intron_variant; upstream_gene_variant	1.0[CEU]
rs690276	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs10518820	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.832[TSI]
rs2467739	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 0.945[GIH]; 1.0[JPT]; 1.0[LWK]; 0.948[MEX]; 0.881[MKK]; 0.959[TSI]; 1.0[YRI]
rs690512	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.953[CHB]; 1.0[JPT]
rs529611	intron_variant; upstream_gene_variant	0.954[CHB]; 0.878[CHD]; 1.0[JPT]
rs956391	downstream_gene_variant	0.878[TSI]
rs2444251	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs2444032	intron_variant; nc_transcript_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 0.925[LWK]; 0.948[MEX]; 0.881[MKK]; 0.959[TSI]; 1.0[YRI]
rs2444250	downstream_gene_variant; intron_variant; nc_transcript_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs12443102	NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CEU]
rs693510	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs2242069	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.936[ASW]; 1.0[CHB]; 0.975[CHD]; 0.945[GIH]; 1.0[JPT]; 1.0[LWK]; 0.948[MEX]; 0.88[MKK]; 1.0[YRI]
rs526450	downstream_gene_variant; upstream_gene_variant	0.805[GIH]; 0.856[MEX]; 0.918[TSI]
rs572837	3_prime_UTR_variant; downstream_gene_variant	0.953[JPT]
rs3742969	intron_variant; synonymous_variant; upstream_gene_variant	0.829[GIH]; 0.856[MEX]; 0.806[MKK]; 0.913[TSI]
rs2251844	downstream_gene_variant; intron_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs694985	intron_variant	0.848[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs2470134	downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CEU]
rs2439	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.916[TSI]
rs2470121	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CEU]
rs486301	downstream_gene_variant; intron_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs2467736	downstream_gene_variant; intron_variant; nc_transcript_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 0.925[LWK]; 1.0[MEX]; 0.881[MKK]; 0.959[TSI]; 1.0[YRI]
rs1079309	intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs496584	intron_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs2467738	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 1.0[JPT]
rs28495368	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.877[TSI]
rs2927072	3_prime_UTR_variant; downstream_gene_variant; intron_variant	0.865[CEU]; 0.839[TSI]
rs3097773	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; splice_region_variant; synonymous_variant; upstream_gene_variant	1.0[CEU]; 0.905[JPT]; 1.0[MEX]; 0.913[TSI]
rs16957680	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.942[YRI]
rs2245715	missense_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs495175	intron_variant; nc_transcript_variant; upstream_gene_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs884704	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.81[ASW]; 1.0[GIH]; 0.812[TSI]
rs560191	missense_variant; nc_transcript_variant; non_coding_exon_variant	1.0[CHB]; 1.0[JPT]
rs7173487	intron_variant; nc_transcript_variant; upstream_gene_variant	0.848[CEU]; 0.948[MEX]; 0.918[TSI]
rs1058298	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.853[CHD]
rs6493085	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.972[GIH]; 0.856[MEX]; 0.918[TSI]
rs1549525	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.894[GIH]; 0.856[MEX]; 0.806[MKK]; 0.918[TSI]
rs537115	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[ASW]; 1.0[CHB]; 0.975[CHD]; 0.916[GIH]; 1.0[JPT]; 1.0[LWK]; 0.946[MEX]; 0.881[MKK]; 0.959[TSI]; 1.0[YRI]
rs2439831	intron_variant; nc_transcript_variant; splice_region_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 1.0[MEX]; 0.918[TSI]
rs690472	intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs480108	synonymous_variant	0.953[JPT]
rs7173383	intron_variant; nc_transcript_variant	0.801[LWK]; 1.0[YRI]
rs1060939	synonymous_variant	0.953[JPT]
rs523156	intron_variant	0.953[JPT]
rs2447208	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.877[TSI]
rs17780417	downstream_gene_variant; intron_variant	0.942[YRI]
rs690466	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs2255051	downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs478104	nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.805[GIH]; 0.856[MEX]; 0.878[TSI]
rs1095386		0.814[ASW]; 0.831[GIH]; 0.87[LWK]; 0.856[MEX]; 0.918[TSI]; 0.942[YRI]
rs484029	downstream_gene_variant; upstream_gene_variant	0.831[GIH]; 0.844[MEX]; 0.918[TSI]
rs689835	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs3101443	intron_variant; upstream_gene_variant	1.0[CEU]
rs2899082	3_prime_UTR_variant; NMD_transcript_variant; intron_variant	0.848[CEU]; 0.972[GIH]; 0.9[MEX]; 0.806[MKK]; 0.918[TSI]
rs1814538	intron_variant; nc_transcript_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 0.925[LWK]; 1.0[MEX]; 0.878[MKK]; 0.959[TSI]; 1.0[YRI]
rs488756		0.831[GIH]
rs16957730	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[YRI]
rs3809481	5_prime_UTR_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.848[CEU]; 0.859[GIH]; 0.848[MEX]; 0.918[TSI]
rs493377	intron_variant; nc_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs690367	NMD_transcript_variant; nc_transcript_variant; non_coding_exon_variant; synonymous_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs2244981	intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs689781	intron_variant; nc_transcript_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 0.925[LWK]; 1.0[MEX]; 0.881[MKK]; 0.918[TSI]; 1.0[YRI]
rs689647	missense_variant; nc_transcript_variant; non_coding_exon_variant	0.937[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 1.0[GIH]; 1.0[JPT]; 0.925[LWK]; 1.0[MEX]; 0.881[MKK]; 0.918[TSI]; 1.0[YRI]
rs12912744	NMD_transcript_variant; downstream_gene_variant; intron_variant; missense_variant; stop_gained; upstream_gene_variant	0.942[YRI]
rs689754	intron_variant; nc_transcript_variant	0.848[CEU]; 0.907[CHB]
rs7181545		0.942[YRI]
rs527921	intron_variant; nc_transcript_variant	0.848[CEU]; 0.888[GIH]; 1.0[MEX]; 0.959[TSI]
rs12911740	intron_variant; nc_transcript_variant	0.801[LWK]; 1.0[YRI]
rs2447211	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CEU]
rs506120	intron_variant; nc_transcript_variant; upstream_gene_variant	0.954[CHB]; 0.95[CHD]; 1.0[JPT]
rs2255042	intron_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs542898	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs8042868	NMD_transcript_variant; downstream_gene_variant; intron_variant; missense_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.837[TSI]
rs689767	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs999047	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[GIH]; 0.9[MEX]; 0.806[MKK]; 0.812[TSI]
rs2467741	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs17723479		0.942[YRI]
rs689826	intron_variant; nc_transcript_variant; upstream_gene_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs4075674	downstream_gene_variant	0.848[CEU]; 0.972[GIH]; 0.897[MEX]; 0.918[TSI]
rs2920781	NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant	1.0[CEU]; 1.0[MEX]; 0.839[TSI]
rs17780920	intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.942[YRI]
rs570933	downstream_gene_variant	0.953[JPT]
rs2444029	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs689797	3_prime_UTR_variant; downstream_gene_variant	0.953[JPT]
rs2439850	downstream_gene_variant; intron_variant; nc_transcript_variant	0.825[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs7177892		0.942[YRI]
rs694725	intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs2278860	NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.848[CEU]; 0.972[GIH]; 0.9[MEX]; 0.806[MKK]; 0.918[TSI]
rs544122	intron_variant; nc_transcript_variant	0.848[CEU]
rs2467737	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 1.0[JPT]
rs3742971	5_prime_UTR_variant; upstream_gene_variant	0.919[GIH]; 0.856[MEX]; 0.806[MKK]; 0.918[TSI]
rs2447196	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.918[TSI]
rs7180812	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.942[YRI]
rs2260160	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1.0[CEU]; 1.0[MEX]; 0.839[TSI]
rs2255440	intron_variant	1.0[CEU]; 0.953[JPT]; 1.0[MEX]; 0.918[TSI]
rs2251538	intron_variant; nc_transcript_variant	0.825[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs524527	downstream_gene_variant; upstream_gene_variant	0.805[GIH]; 0.856[MEX]; 0.918[TSI]
rs8039638	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.81[ASW]; 0.971[GIH]; 0.806[MKK]
rs2253708	intron_variant; nc_transcript_variant	0.848[CEU]; 1.0[CHB]; 1.0[JPT]
rs536313	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.975[CHD]; 1.0[JPT]
rs2412780	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.848[CEU]; 0.972[GIH]; 0.9[MEX]; 0.806[MKK]; 0.918[TSI]
rs2412779	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.848[CEU]; 0.972[GIH]; 0.897[MEX]; 0.806[MKK]; 0.918[TSI]
rs1837960	3_prime_UTR_variant; downstream_gene_variant; intron_variant	0.936[ASW]; 0.915[GIH]; 0.807[TSI]
rs2447193	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CEU]
rs2253268	intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.975[CHD]; 0.953[JPT]
rs2245790	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[ASW]; 0.848[CEU]; 1.0[CHB]; 0.975[CHD]; 0.945[GIH]; 1.0[JPT]; 1.0[LWK]; 0.948[MEX]; 0.959[TSI]; 1.0[YRI]