Variant report

Variant	rs34638
Chromosome Location	chr5:60350487-60350488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 197 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10064187	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10076937	0.86[ASN][1000 genomes]
rs1020371	0.80[ASN][1000 genomes]
rs1038144	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10471502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11744756	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11957772	1.00[ASN][1000 genomes]
rs124898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12518865	1.00[ASN][1000 genomes]
rs12522154	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13155076	0.86[ASN][1000 genomes]
rs13168191	1.00[ASN][1000 genomes]
rs1382914	1.00[ASN][1000 genomes]
rs158564	1.00[ASN][1000 genomes]
rs158570	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs158571	0.97[ASN][1000 genomes]
rs158572	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs158696	0.94[ASN][1000 genomes]
rs158697	0.94[ASN][1000 genomes]
rs158699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs158700	0.94[ASN][1000 genomes]
rs158914	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158915	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs158918	0.91[ASN][1000 genomes]
rs158919	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs158921	1.00[JPT][hapmap]
rs158922	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158923	1.00[ASN][1000 genomes]
rs158924	1.00[ASN][1000 genomes]
rs158927	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158929	0.91[ASN][1000 genomes]
rs158931	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs158932	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs158933	0.97[ASN][1000 genomes]
rs158934	0.97[ASN][1000 genomes]
rs158935	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs158936	0.97[ASN][1000 genomes]
rs158937	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs158938	0.81[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159358	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs159371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159374	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159376	0.94[ASN][1000 genomes]
rs159377	0.94[ASN][1000 genomes]
rs159378	0.94[ASN][1000 genomes]
rs159380	0.94[ASN][1000 genomes]
rs162228	0.91[ASN][1000 genomes]
rs162234	1.00[ASN][1000 genomes]
rs162238	1.00[ASN][1000 genomes]
rs162241	1.00[ASN][1000 genomes]
rs162242	1.00[ASN][1000 genomes]
rs162243	0.91[ASN][1000 genomes]
rs162244	1.00[ASN][1000 genomes]
rs162246	0.91[ASN][1000 genomes]
rs162248	1.00[ASN][1000 genomes]
rs162251	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168710	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878547	0.94[ASN][1000 genomes]
rs16878548	0.94[ASN][1000 genomes]
rs169700	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172348	1.00[ASN][1000 genomes]
rs172945	1.00[ASN][1000 genomes]
rs1820082	0.81[ASN][1000 genomes]
rs182410	0.94[ASN][1000 genomes]
rs1867598	0.80[ASN][1000 genomes]
rs187459	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989653	0.94[ASN][1000 genomes]
rs2080869	1.00[ASN][1000 genomes]
rs2120954	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2120955	0.91[ASN][1000 genomes]
rs2263514	1.00[ASN][1000 genomes]
rs2270822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs248677	1.00[ASN][1000 genomes]
rs248682	1.00[ASN][1000 genomes]
rs248683	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248685	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs248688	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545475	0.94[ASN][1000 genomes]
rs2545478	0.89[ASN][1000 genomes]
rs2545493	0.85[ASN][1000 genomes]
rs2545503	0.94[ASN][1000 genomes]
rs256375	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256376	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590570	0.86[ASN][1000 genomes]
rs2619890	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619893	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650512	1.00[ASN][1000 genomes]
rs2650517	1.00[ASN][1000 genomes]
rs2694518	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2694528	0.94[ASN][1000 genomes]
rs2694530	1.00[ASN][1000 genomes]
rs2694531	1.00[ASN][1000 genomes]
rs28407266	0.91[ASN][1000 genomes]
rs290503	1.00[ASN][1000 genomes]
rs290506	1.00[ASN][1000 genomes]
rs290507	1.00[ASN][1000 genomes]
rs290511	0.94[ASN][1000 genomes]
rs290513	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290514	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290515	0.91[ASN][1000 genomes]
rs2928244	0.83[EUR][1000 genomes]
rs2950235	1.00[ASN][1000 genomes]
rs295522	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs295524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295531	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295533	1.00[ASN][1000 genomes]
rs295551	0.94[ASN][1000 genomes]
rs295559	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295560	0.94[ASN][1000 genomes]
rs295561	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295563	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295564	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295566	0.91[ASN][1000 genomes]
rs295569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs295573	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295578	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101879	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108388	1.00[ASN][1000 genomes]
rs3117	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs329622	1.00[ASN][1000 genomes]
rs329623	1.00[ASN][1000 genomes]
rs329624	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329625	1.00[ASN][1000 genomes]
rs329626	1.00[ASN][1000 genomes]
rs34591	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34592	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593	1.00[ASN][1000 genomes]
rs34594	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34610	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34614	0.94[ASN][1000 genomes]
rs34621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34624	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs34636	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34637	0.94[ASN][1000 genomes]
rs34639	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34643	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35546392	0.83[ASN][1000 genomes]
rs35617853	0.80[ASN][1000 genomes]
rs35766700	0.86[ASN][1000 genomes]
rs35948426	0.86[ASN][1000 genomes]
rs39661	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs40084	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40421	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141502	1.00[ASN][1000 genomes]
rs4235483	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4235484	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs42437	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546327	0.80[ASN][1000 genomes]
rs4647045	1.00[CHB][hapmap]
rs4647102	0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4647138	0.86[ASN][1000 genomes]
rs4647139	0.86[ASN][1000 genomes]
rs4647151	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4647162	0.81[ASN][1000 genomes]
rs4699963	0.80[ASN][1000 genomes]
rs4699967	0.88[ASN][1000 genomes]
rs4700406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409036	1.00[ASN][1000 genomes]
rs59292447	0.88[ASN][1000 genomes]
rs59797139	0.83[ASN][1000 genomes]
rs6862622	0.88[ASN][1000 genomes]
rs6863749	0.88[ASN][1000 genomes]
rs6868884	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869454	0.88[ASN][1000 genomes]
rs6878124	1.00[ASN][1000 genomes]
rs6885989	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6886481	1.00[ASN][1000 genomes]
rs6893210	0.88[ASN][1000 genomes]
rs723276	1.00[ASN][1000 genomes]
rs7701839	0.85[ASN][1000 genomes]
rs7712364	0.88[ASN][1000 genomes]
rs7718028	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7723754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs810883	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs810884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9291702	0.94[ASN][1000 genomes]
rs929780	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs973304	0.80[ASN][1000 genomes]
rs976080	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9763418	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs976581	1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34638	ELOVL7	cis	parietal	SCAN
rs34638	ERCC8	cis	multi-tissue	Pritchard
rs34638	mimitin	cis	multi-tissue	Pritchard
rs34638	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60324600-60354000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
3	chr5:60344800-60353400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:60345600-60350800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:60346800-60350600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:60347000-60350600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:60347200-60379200	Weak transcription	Ovary	ovary
8	chr5:60347400-60351400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:60347400-60353000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:60347400-60356000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:60347800-60353000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:60349200-60352800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:60349400-60353000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:60349400-60370800	Weak transcription	HSMM	muscle
15	chr5:60349600-60353000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:60350200-60350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:60350400-60350600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:60350400-60362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:60350400-60371400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links