Variant report

Variant	rs7094041
Chromosome Location	chr10:4982478-4982479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10159511	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10904362	0.88[JPT][hapmap]
rs10904367	0.88[JPT][hapmap]
rs10904368	0.88[JPT][hapmap]
rs11252804	0.85[JPT][hapmap]
rs11252824	0.89[JPT][hapmap]
rs11252836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11252839	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12249166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12251296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12253332	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12255269	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12258506	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12258513	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12261928	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1869218	0.88[JPT][hapmap]
rs1901644	0.88[JPT][hapmap]
rs1993181	0.88[JPT][hapmap]
rs2167703	0.88[JPT][hapmap]
rs2397984	0.88[JPT][hapmap]
rs2924265	0.88[JPT][hapmap]
rs2924267	0.88[JPT][hapmap]
rs2961568	0.88[JPT][hapmap]
rs2961571	0.88[JPT][hapmap]
rs2961576	0.88[JPT][hapmap]
rs2961578	0.88[JPT][hapmap]
rs2961586	0.88[JPT][hapmap]
rs2961591	0.88[JPT][hapmap]
rs3812665	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4277002	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4880693	0.88[JPT][hapmap]
rs4880698	0.82[JPT][hapmap]
rs4881367	0.85[JPT][hapmap]
rs6601873	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs67865366	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7067785	0.88[JPT][hapmap]
rs7081411	0.88[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7089338	0.88[JPT][hapmap]
rs7098390	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72769959	0.80[EUR][1000 genomes]
rs7358055	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7358080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7894644	0.88[JPT][hapmap]
rs7896709	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7900816	0.86[JPT][hapmap]
rs7920935	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7921097	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv894793	chr10:4935482-4988818	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7094041	ATP5C1	cis	parietal	SCAN
rs7094041	AKR1C2	cis	normal skin	skin_eQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4967800-4983800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:4968600-4990800	Weak transcription	Primary T cells from cord blood	blood
3	chr10:4969800-4983600	Weak transcription	Adipose Nuclei	Adipose
4	chr10:4973000-4984800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:4973000-5005600	Weak transcription	Left Ventricle	heart
6	chr10:4973200-4983800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:4973200-4994800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:4974000-4983200	Weak transcription	Right Ventricle	heart
9	chr10:4974000-4990600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:4974200-4986200	Weak transcription	Psoas Muscle	Psoas
11	chr10:4974200-4990600	Weak transcription	Esophagus	oesophagus
12	chr10:4974600-4985400	Weak transcription	Fetal Stomach	stomach
13	chr10:4977800-4988200	Weak transcription	Pancreas	Pancrea
14	chr10:4980600-4984200	Enhancers	Fetal Intestine Small	intestine
15	chr10:4980800-4984200	Enhancers	Fetal Intestine Large	intestine
16	chr10:4981000-4984200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:4981000-4986000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:4981200-4984000	Enhancers	K562	blood
19	chr10:4981200-4984600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:4981400-4982600	Enhancers	HSMM	muscle
21	chr10:4981400-4985600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:4981400-4985600	Enhancers	HMEC	breast
23	chr10:4981400-4987600	Enhancers	Hela-S3	cervix
24	chr10:4981600-4983200	Weak transcription	Aorta	Aorta
25	chr10:4981600-4985400	Weak transcription	Ovary	ovary
26	chr10:4981800-4982600	Enhancers	HSMMtube	muscle
27	chr10:4982000-4989600	Enhancers	HepG2	liver
28	chr10:4982200-4982600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:4982200-4982600	Enhancers	Liver	Liver
30	chr10:4982200-4982600	Flanking Active TSS	NHEK	skin
31	chr10:4982200-4983400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:4982200-4983600	Weak transcription	HUVEC	blood vessel
33	chr10:4982200-4983600	Weak transcription	Osteobl	bone
34	chr10:4982200-4987400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:4982400-4982600	Enhancers	Lung	lung
36	chr10:4982400-4983200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:4982400-4983400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:4982400-4983400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:4982400-4983400	Weak transcription	Stomach Mucosa	stomach
40	chr10:4982400-4984000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:4982400-4984000	Enhancers	A549	lung
42	chr10:4982400-4984000	Weak transcription	NHDF-Ad	bronchial

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