Variant report

Variant	rs11934632
Chromosome Location	chr4:47877840-47877841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47873831..47876676-chr4:47876808..47878387,2	K562	blood:
2	chr4:47876934..47878897-chr4:47913738..47916807,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10008818	0.80[ASN][1000 genomes]
rs1012844	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs10517201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938509	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11722700	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11737879	0.86[ASN][1000 genomes]
rs11933101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940319	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11940441	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501949	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505333	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506863	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509420	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12509520	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510304	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512884	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512988	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440221	0.81[ASN][1000 genomes]
rs1440224	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs1465885	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860663	0.86[ASN][1000 genomes]
rs17463534	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573717	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1822029	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965804	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1992326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165263	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882949	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34449323	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4031458	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4405986	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4435717	0.80[ASN][1000 genomes]
rs4475122	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518214	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695280	0.86[ASN][1000 genomes]
rs4695317	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55844485	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56084299	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56384707	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56686194	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56971681	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57159058	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60535228	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62298261	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62298266	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62298267	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62298302	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62298303	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62298344	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62299256	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62299257	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62299258	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62299259	0.92[ASN][1000 genomes]
rs62301160	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62301161	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62301163	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447585	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447591	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66901846	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816253	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6819172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820636	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833422	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6844066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848667	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857248	1.00[YRI][hapmap]
rs7654965	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11934632	RP11-121C2.2	cis	Whole Blood	GTEx
rs11934632	CORIN	cis	Whole Blood	GTEx
rs11934632	NFXL1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47839800-47885800	Weak transcription	Lung	lung
2	chr4:47840000-47886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:47840200-47881600	Weak transcription	Stomach Mucosa	stomach
4	chr4:47840200-47885200	Weak transcription	Aorta	Aorta
5	chr4:47840200-47885800	Weak transcription	Pancreas	Pancrea
6	chr4:47841800-47880000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:47843800-47897000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:47860600-47878200	Weak transcription	Hela-S3	cervix
9	chr4:47861200-47893200	Weak transcription	Gastric	stomach
10	chr4:47865000-47880400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:47865200-47885800	Weak transcription	Thymus	Thymus
12	chr4:47865400-47913400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:47865600-47894000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:47869200-47885200	Weak transcription	Fetal Stomach	stomach
15	chr4:47870800-47882400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:47871200-47885600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:47872400-47887800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:47872400-47911600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:47873000-47878400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:47873400-47888200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr4:47873400-47913400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:47873600-47910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:47874400-47879800	Strong transcription	Primary T cells from cord blood	blood
24	chr4:47874400-47882000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr4:47874400-47889000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:47874400-47913400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:47874400-47913600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:47874600-47879400	Strong transcription	Brain Hippocampus Middle	brain
29	chr4:47874600-47880800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:47874600-47881000	Strong transcription	Placenta	Placenta
31	chr4:47874600-47881800	Strong transcription	HMEC	breast
32	chr4:47874600-47888400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:47874600-47888800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:47874600-47889000	Strong transcription	HSMM	muscle
35	chr4:47874600-47889200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:47874800-47879200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:47874800-47880000	Strong transcription	Osteobl	bone
38	chr4:47874800-47880800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr4:47874800-47880800	Strong transcription	A549	lung
40	chr4:47874800-47881000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:47874800-47882000	Strong transcription	NH-A	brain
42	chr4:47874800-47882400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr4:47874800-47886800	Strong transcription	HUVEC	blood vessel
44	chr4:47874800-47888400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:47875000-47879200	Strong transcription	Fetal Thymus	thymus
46	chr4:47875200-47879200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr4:47875600-47880800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:47875800-47878200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:47875800-47879600	Strong transcription	Fetal Intestine Large	intestine
50	chr4:47875800-47880800	Strong transcription	K562	blood

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