Variant report

Variant	rs3902925
Chromosome Location	chr10:5050622-5050623
allele	C/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	SP1	chr10:5050407-5052312	A549	lung:	n/a	n/a
2	SP1	chr10:5050569-5052173	A549	lung:	n/a	n/a
3	TCF12	chr10:5050554-5052073	A549	lung:	n/a	n/a
4	FOXA1	chr10:5050503-5051869	HepG2	liver:	n/a	chr10:5051463-5051478 chr10:5051528-5051540
5	POLR2A	chr10:5050514-5050695	A549	lung:	n/a	n/a
6	FOXA2	chr10:5050429-5050918	A549	lung:	n/a	n/a
7	FOXA2	chr10:5050409-5051932	A549	lung:	n/a	chr10:5051528-5051540
8	POLR2A	chr10:5050480-5050723	A549	lung:	n/a	n/a
9	POLR2A	chr10:5050487-5050699	A549	lung:	n/a	n/a
10	EP300	chr10:5050582-5050893	HepG2	liver:	n/a	chr10:5050628-5050635

No.	Distal block	Cell Line	Cell type
1	chr10:5049047..5051331-chr10:5062456..5064553,2	MCF-7	breast:
2	chr10:4997960..5000911-chr10:5049814..5051321,2	MCF-7	breast:
3	chr10:5048912..5051298-chr10:5054151..5056215,2	MCF-7	breast:

Variant related genes	Relation type
AKR1C2	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10795213	0.81[CEU][hapmap]
rs11252834	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs12268038	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2904802	0.81[CEU][hapmap]
rs3812666	0.92[CEU][hapmap]
rs3812667	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs4255441	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4323780	0.81[CEU][hapmap]
rs4339935	0.96[MEX][hapmap]
rs4427477	0.85[CEU][hapmap]
rs4528219	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4550138	0.89[CEU][hapmap]
rs4596966	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6601872	0.92[CEU][hapmap]
rs6601875	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7076643	0.85[CEU][hapmap]
rs7081421	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7093917	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7096506	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7901384	0.92[CEU][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs7914666	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7921514	0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs8181448	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv894794	chr10:4972761-5121745	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv549884	chr10:5037926-5065248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3902925	UCN3	cis	cerebellum	SCAN
rs3902925	ATP5C1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5024400-5056800	Weak transcription	Esophagus	oesophagus
2	chr10:5024800-5051400	Weak transcription	Fetal Intestine Small	intestine
3	chr10:5046000-5050800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:5046000-5051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:5047600-5051000	Weak transcription	NHEK	skin
6	chr10:5047800-5050800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:5047800-5050800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:5047800-5051200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:5050200-5051200	Enhancers	HepG2	liver
10	chr10:5050400-5051400	Flanking Active TSS	A549	lung
11	chr10:5050400-5053200	Enhancers	Hela-S3	cervix
12	chr10:5050600-5051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:5050600-5052000	Enhancers	Pancreas	Pancrea
14	chr10:5050600-5052000	Enhancers	HMEC	breast
15	chr10:5050600-5052200	Enhancers	Stomach Mucosa	stomach

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