Variant report

Variant	rs6872959
Chromosome Location	chr5:43732184-43732185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 185 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10035353	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10039531	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10042852	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10045029	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10050726	1.00[ASN][1000 genomes]
rs10054514	0.96[ASN][1000 genomes]
rs10055374	0.96[ASN][1000 genomes]
rs10059603	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10059613	0.95[ASN][1000 genomes]
rs10062920	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064711	0.95[ASN][1000 genomes]
rs10065107	0.90[ASN][1000 genomes]
rs10066806	0.94[ASN][1000 genomes]
rs10068765	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10069201	0.87[ASW][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.80[ASN][1000 genomes]
rs10069341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071683	0.95[ASN][1000 genomes]
rs10073552	0.96[ASN][1000 genomes]
rs10077102	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10077972	0.95[ASN][1000 genomes]
rs10079935	0.95[ASN][1000 genomes]
rs10155531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461744	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10461745	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461746	0.87[EUR][1000 genomes]
rs10461747	0.97[ASN][1000 genomes]
rs10461748	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10462056	0.97[ASN][1000 genomes]
rs10462057	0.97[ASN][1000 genomes]
rs10472386	0.96[ASN][1000 genomes]
rs10472388	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332274	0.95[ASN][1000 genomes]
rs12697461	0.90[ASN][1000 genomes]
rs12697462	0.90[ASN][1000 genomes]
rs13161149	1.00[MEX][hapmap]
rs13161165	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13163981	0.90[ASN][1000 genomes]
rs13165656	0.96[ASN][1000 genomes]
rs13173365	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13174983	0.84[ASN][1000 genomes]
rs13177579	0.95[ASN][1000 genomes]
rs13178040	0.97[ASN][1000 genomes]
rs13178059	0.90[ASN][1000 genomes]
rs13179099	0.91[ASN][1000 genomes]
rs13182721	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183124	0.93[ASN][1000 genomes]
rs13183238	0.93[ASN][1000 genomes]
rs13184712	0.97[ASN][1000 genomes]
rs13187446	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13187695	0.96[ASN][1000 genomes]
rs13356232	1.00[CEU][hapmap]
rs13357293	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13361045	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16873432	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16873435	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16873438	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16873471	0.93[ASN][1000 genomes]
rs16873502	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs2042950	1.00[MEX][hapmap]
rs2303732	0.96[ASN][1000 genomes]
rs2303733	0.95[ASN][1000 genomes]
rs28520030	0.96[ASN][1000 genomes]
rs34003086	0.93[ASN][1000 genomes]
rs34028586	0.97[ASN][1000 genomes]
rs34132518	0.95[ASN][1000 genomes]
rs34184759	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34289650	0.95[ASN][1000 genomes]
rs34315545	0.90[ASN][1000 genomes]
rs34325384	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34361740	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34378343	0.90[ASN][1000 genomes]
rs34420640	0.95[ASN][1000 genomes]
rs34435369	0.95[ASN][1000 genomes]
rs34571724	0.91[ASN][1000 genomes]
rs34748969	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34814715	0.96[ASN][1000 genomes]
rs34844158	0.96[ASN][1000 genomes]
rs34871596	0.86[ASN][1000 genomes]
rs34897533	0.94[ASN][1000 genomes]
rs34902970	0.95[ASN][1000 genomes]
rs35023467	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35047682	0.90[ASN][1000 genomes]
rs35072002	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35151191	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35228179	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35249562	0.97[ASN][1000 genomes]
rs35383935	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35388758	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35429460	0.94[ASN][1000 genomes]
rs35442919	0.96[ASN][1000 genomes]
rs35580004	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35592802	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35606071	0.93[ASN][1000 genomes]
rs35609488	0.94[ASN][1000 genomes]
rs35663171	0.91[ASN][1000 genomes]
rs35672591	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35687864	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35696038	0.92[ASN][1000 genomes]
rs35697559	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35773128	0.90[ASN][1000 genomes]
rs35818459	0.95[ASN][1000 genomes]
rs35842681	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35867146	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35955731	0.96[ASN][1000 genomes]
rs3764980	1.00[MEX][hapmap]
rs3805720	1.00[MEX][hapmap]
rs3805722	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3828696	0.96[ASN][1000 genomes]
rs3884574	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3884575	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4318792	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4380668	0.96[ASN][1000 genomes]
rs4382179	0.96[ASN][1000 genomes]
rs4403180	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449542	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4476731	0.96[ASN][1000 genomes]
rs4484444	0.90[ASN][1000 genomes]
rs4493678	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367650	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62367658	0.91[ASN][1000 genomes]
rs62368560	0.81[EUR][1000 genomes]
rs62368566	0.83[AFR][1000 genomes]
rs62368574	0.93[ASN][1000 genomes]
rs62368575	0.93[ASN][1000 genomes]
rs62368577	0.95[ASN][1000 genomes]
rs62368578	0.95[ASN][1000 genomes]
rs62368581	0.96[ASN][1000 genomes]
rs62368584	0.96[ASN][1000 genomes]
rs62368594	0.89[EUR][1000 genomes]
rs62368632	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62368636	0.80[ASN][1000 genomes]
rs62368637	0.80[ASN][1000 genomes]
rs62368638	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62368640	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368641	0.97[ASN][1000 genomes]
rs62368655	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62369476	0.97[ASN][1000 genomes]
rs62369480	0.96[ASN][1000 genomes]
rs6451719	1.00[MEX][hapmap]
rs6451722	0.81[ASN][1000 genomes]
rs6863699	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868008	0.87[ASN][1000 genomes]
rs6869748	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6871373	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6872531	0.83[ASN][1000 genomes]
rs6874033	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6875118	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6875365	0.90[ASN][1000 genomes]
rs6875400	0.90[ASN][1000 genomes]
rs6878821	0.96[ASN][1000 genomes]
rs6892300	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893250	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6895383	0.96[ASN][1000 genomes]
rs6897045	0.92[ASN][1000 genomes]
rs6897559	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6898436	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs71629185	0.83[EUR][1000 genomes]
rs71629189	0.93[ASN][1000 genomes]
rs71629192	0.96[ASN][1000 genomes]
rs71629193	0.94[ASN][1000 genomes]
rs716960	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs73753626	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73753650	0.90[ASN][1000 genomes]
rs73753651	0.90[ASN][1000 genomes]
rs73753652	0.90[ASN][1000 genomes]
rs7708386	0.95[ASN][1000 genomes]
rs7711370	1.00[ASN][1000 genomes]
rs7713661	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7713856	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7717645	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7717974	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7721405	0.90[ASN][1000 genomes]
rs7723874	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7724195	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7725789	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733259	0.96[ASN][1000 genomes]
rs7737947	1.00[CEU][hapmap]
rs9292896	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9784611	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9918185	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv3471542	chr5:43665651-43824536	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3471543	chr5:43665767-43824443	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537740	chr5:43729430-43782732	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6872959	NNT	cis	lymphoblastoid	seeQTL
rs6872959	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs6872959	NNT	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43730600-43732200	Enhancers	Stomach Mucosa	stomach
2	chr5:43731400-43732400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links