Variant report

Variant	rs4339935
Chromosome Location	chr10:4986044-4986045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:4984421..4986363-chr10:4988529..4990778,2	K562	blood:
2	chr10:4984238..4986431-chr10:4987413..4989346,2	MCF-7	breast:
3	chr10:4984421..4986595-chr10:4988529..4991058,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10159511	0.82[JPT][hapmap]
rs12255269	0.85[JPT][hapmap]
rs12268038	0.89[CHB][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes]
rs2904804	0.82[CEU][hapmap]
rs3812667	0.87[MEX][hapmap]
rs3902925	0.96[MEX][hapmap]
rs4255441	0.89[CHB][hapmap];0.80[AMR][1000 genomes]
rs4342925	0.80[AMR][1000 genomes]
rs4364963	0.81[ASN][1000 genomes]
rs4483487	0.80[AMR][1000 genomes]
rs4528219	0.83[CHB][hapmap];0.92[MEX][hapmap]
rs4596966	0.89[CHB][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs6601875	0.88[CHB][hapmap];0.84[AMR][1000 genomes]
rs6601876	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7081411	0.82[JPT][hapmap];0.81[LWK][hapmap]
rs7081421	0.81[ASW][hapmap];0.89[CHB][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7093917	0.89[CHB][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes]
rs7096506	0.88[CHB][hapmap]
rs7098390	0.82[JPT][hapmap]
rs7100824	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7901384	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs7914666	0.89[CHB][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap]
rs7921514	0.81[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4339935	AKR1C1	cis	multi-tissue	Pritchard
rs4339935	AKR1C1	cis	Whole Blood	GTEx
rs4339935	ATP5C1	cis	parietal	SCAN
rs4339935	C9orf43	trans	cerebellum	SCAN
rs4339935	BC014579	cis	multi-tissue	Pritchard
rs4339935	AKR1C2	cis	parietal	SCAN
rs4339935	AKR1C1	cis	Liver	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4968600-4990800	Weak transcription	Primary T cells from cord blood	blood
2	chr10:4973000-5005600	Weak transcription	Left Ventricle	heart
3	chr10:4973200-4994800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:4974000-4990600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:4974200-4986200	Weak transcription	Psoas Muscle	Psoas
6	chr10:4974200-4990600	Weak transcription	Esophagus	oesophagus
7	chr10:4977800-4988200	Weak transcription	Pancreas	Pancrea
8	chr10:4981400-4987600	Enhancers	Hela-S3	cervix
9	chr10:4982000-4989600	Enhancers	HepG2	liver
10	chr10:4982200-4987400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:4983200-4986400	Enhancers	HSMMtube	muscle
12	chr10:4983200-4987000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:4983400-4987200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr10:4983600-4987200	Enhancers	Osteobl	bone
15	chr10:4983600-4991600	Enhancers	Adipose Nuclei	Adipose
16	chr10:4983800-4986400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr10:4983800-4986600	Enhancers	Liver	Liver
18	chr10:4983800-4987000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr10:4984000-4986400	Enhancers	NHLF	lung
20	chr10:4984000-4987000	Enhancers	HSMM	muscle
21	chr10:4984000-4988000	Enhancers	NHDF-Ad	bronchial
22	chr10:4984000-4990400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:4984200-4986200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:4984200-4987200	Weak transcription	Fetal Intestine Small	intestine
25	chr10:4984200-4989600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr10:4984600-4986600	Enhancers	Fetal Muscle Leg	muscle
27	chr10:4984800-4986600	Enhancers	Stomach Smooth Muscle	stomach
28	chr10:4984800-4988400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr10:4985000-4987200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:4985000-4989000	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:4985000-4989200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:4985200-4986800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:4985400-4986600	Enhancers	Fetal Stomach	stomach
34	chr10:4985400-4986600	Enhancers	Ovary	ovary
35	chr10:4985400-4988000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:4985400-4990600	Weak transcription	Right Atrium	heart
37	chr10:4985600-4989000	Weak transcription	Stomach Mucosa	stomach
38	chr10:4985600-4989000	Weak transcription	NHEK	skin
39	chr10:4985600-4989200	Weak transcription	HMEC	breast
40	chr10:4985600-4989400	Weak transcription	NH-A	brain
41	chr10:4985600-4989800	Weak transcription	HUVEC	blood vessel
42	chr10:4985600-4990400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:4985800-4986200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:4985800-4986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:4985800-4986200	Enhancers	Fetal Lung	lung
46	chr10:4985800-4989400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:4986000-4986400	Enhancers	Aorta	Aorta
48	chr10:4986000-4986400	ZNF genes & repeats	A549	lung
49	chr10:4986000-4986800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr10:4986000-4987600	Enhancers	HUES48 Cell Line	embryonic stem cell

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