Variant report

Variant	rs16890309
Chromosome Location	chr6:37973613-37973614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:37973555-37973869	HepG2	liver:	n/a	chr6:37973767-37973782
2	FOXA1	chr6:37973574-37973877	T-47D	breast:	n/a	chr6:37973767-37973782

Variant related genes	Relation type
ENSG00000218521	TF binding region

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10485030	0.85[CHB][hapmap]
rs10498739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10498740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10947702	0.85[CHB][hapmap]
rs10947704	0.85[CHB][hapmap]
rs10947710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11750950	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11751781	0.85[CHB][hapmap]
rs11752521	0.85[CHB][hapmap]
rs11752863	0.93[ASN][1000 genomes]
rs11753054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11755629	0.85[CHB][hapmap]
rs11756713	0.85[CHB][hapmap]
rs11756902	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11757072	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11757323	0.96[ASN][1000 genomes]
rs11758095	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11759483	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs11759725	0.94[ASN][1000 genomes]
rs11759826	0.85[CHB][hapmap]
rs12660221	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12660498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12660732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12660773	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12660922	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12661073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12661109	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12661129	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12661378	0.85[CHB][hapmap]
rs12661480	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12662305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12662426	0.85[CHB][hapmap]
rs12662823	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12663086	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12663207	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12663427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12663957	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12664091	0.85[CHB][hapmap]
rs12664768	0.85[CHB][hapmap]
rs12664900	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13206035	0.85[CHB][hapmap]
rs16890177	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs16890181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs16890215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16890247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16890299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16890301	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs16890305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16890307	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16890341	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16890362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1885324	0.89[CHB][hapmap]
rs2055207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2055208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2064795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2145887	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2273441	0.84[CHB][hapmap]
rs2274090	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2274091	0.84[CHB][hapmap]
rs2395689	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs2395692	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2395693	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2645125	0.82[ASN][1000 genomes]
rs2842510	0.85[CHB][hapmap]
rs2842511	0.90[CHB][hapmap]
rs2842521	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs28740822	0.96[ASN][1000 genomes]
rs34370874	0.96[ASN][1000 genomes]
rs3800364	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3844314	0.85[CHB][hapmap]
rs3852216	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4524602	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55786703	0.99[ASN][1000 genomes]
rs56348433	0.96[ASN][1000 genomes]
rs56390138	0.96[ASN][1000 genomes]
rs56688119	0.81[ASN][1000 genomes]
rs57142729	0.80[ASN][1000 genomes]
rs57160603	0.96[ASN][1000 genomes]
rs57198506	1.00[AMR][1000 genomes]
rs57276677	0.91[ASN][1000 genomes]
rs57458792	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57591988	0.94[ASN][1000 genomes]
rs57911756	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57995712	0.96[ASN][1000 genomes]
rs58084785	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58320470	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58332635	0.80[ASN][1000 genomes]
rs58473303	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58692659	1.00[AMR][1000 genomes]
rs59036086	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59103990	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59649654	1.00[AMR][1000 genomes]
rs59769374	0.96[ASN][1000 genomes]
rs59859268	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59996041	0.98[ASN][1000 genomes]
rs60284537	1.00[AMR][1000 genomes]
rs60404082	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60425175	0.81[ASN][1000 genomes]
rs60508820	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60637081	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60883115	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61090283	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61108907	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61172238	0.81[ASN][1000 genomes]
rs61277916	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61332486	1.00[AMR][1000 genomes]
rs61466900	1.00[AMR][1000 genomes]
rs6458032	0.85[CHB][hapmap]
rs6911716	0.85[CHB][hapmap]
rs71569402	0.83[ASN][1000 genomes]
rs73421436	0.93[ASN][1000 genomes]
rs73421439	0.93[ASN][1000 genomes]
rs752110	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7739801	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs7742226	0.84[CHB][hapmap]
rs7746266	0.84[CHB][hapmap]
rs7748312	0.85[CHB][hapmap]
rs7748392	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7759792	0.85[CHB][hapmap]
rs7764130	0.85[CHB][hapmap]
rs7773419	0.85[CHB][hapmap]
rs7775794	0.85[CHB][hapmap]
rs874095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs876818	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9470772	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470777	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470784	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470794	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs9470798	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2753764	chr6:37963308-37978172	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37956200-37978800	Weak transcription	Primary T cells from cord blood	blood
2	chr6:37957800-37976400	Weak transcription	Aorta	Aorta
3	chr6:37959400-37975600	Weak transcription	Left Ventricle	heart
4	chr6:37960800-37982400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:37962200-37975800	Weak transcription	Liver	Liver
6	chr6:37963000-37975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:37963000-37975800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:37963000-37977600	Weak transcription	Ovary	ovary
9	chr6:37963000-37984800	Weak transcription	Right Atrium	heart
10	chr6:37963000-37995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:37965600-37982200	Weak transcription	Psoas Muscle	Psoas
12	chr6:37965800-37979000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:37967600-37977600	Weak transcription	Primary B cells from cord blood	blood
14	chr6:37969200-37987800	Weak transcription	Fetal Kidney	kidney
15	chr6:37969400-37976400	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:37969400-37977600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:37970800-37984200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:37971000-37976200	Weak transcription	HepG2	liver
19	chr6:37971200-37975800	Weak transcription	Fetal Heart	heart
20	chr6:37972200-37976000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:37972400-37983800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:37972800-37976400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:37973400-37974000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr6:37973600-37974000	Enhancers	Fetal Lung	lung

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