Variant report

Variant	rs4882631
Chromosome Location	chr12:75944907-75944908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75942788..75945762-chr12:75947332..75949083,2	K562	blood:
2	chr12:75942170..75945016-chr12:75945671..75947951,2	MCF-7	breast:
3	chr12:75936274..75938020-chr12:75944642..75947136,2	MCF-7	breast:
4	chr12:75904950..75907035-chr12:75944732..75947463,2	K562	blood:
5	chr12:75939240..75941323-chr12:75943102..75945716,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10748282	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10785195	0.82[EUR][1000 genomes]
rs10785198	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10879929	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879930	0.82[EUR][1000 genomes]
rs10879932	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879933	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879934	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879935	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879936	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879938	0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs11180562	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180575	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180584	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180598	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11180603	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11514051	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11519910	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11520226	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12811250	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697759	0.82[EUR][1000 genomes]
rs17115238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054518	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2366988	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366989	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2886826	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34406885	0.89[EUR][1000 genomes]
rs3847671	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3898937	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4323912	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58886425	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60465677	0.93[EUR][1000 genomes]
rs6582293	0.86[EUR][1000 genomes]
rs7137610	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs7300994	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305673	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7314220	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs733880	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs733881	0.85[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7955264	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7956673	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs7956799	0.81[EUR][1000 genomes]
rs7956953	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958508	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962144	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7962276	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7979460	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979600	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7980713	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634253	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4882631	GLIPR1	cis	cerebellum	SCAN
rs4882631	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4882631	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs4882631	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs4882631	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4882631	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4882631	GLIPR1L2	cis	cerebellum	SCAN
rs4882631	GLIPR1L2	cis	parietal	SCAN
rs4882631	GLIPR1L2	cis	Artery Tibial	GTEx
rs4882631	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs4882631	GLIPR1	cis	parietal	SCAN
rs4882631	GLIPR1L2	cis	Thyroid	GTEx
rs4882631	KRR1	cis	parietal	SCAN
rs4882631	KRR1	cis	cerebellum	SCAN
rs4882631	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs4882631	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs4882631	GLIPR1L1	cis	multi-tissue	Pritchard
rs4882631	RP11-585P4.5	cis	Artery Tibial	GTEx
rs4882631	GLIPR1L2	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75938600-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75942800-75945800	Weak transcription	Fetal Brain Male	brain
3	chr12:75942800-75947400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:75942800-75947400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:75943000-75947200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:75943000-75947200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:75943200-75945200	Enhancers	Fetal Lung	lung
8	chr12:75943400-75945600	Enhancers	HSMMtube	muscle
9	chr12:75943600-75945200	Enhancers	Fetal Kidney	kidney
10	chr12:75943600-75945200	Enhancers	HUVEC	blood vessel
11	chr12:75943800-75945000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:75943800-75945000	Enhancers	Adipose Nuclei	Adipose
13	chr12:75943800-75945000	Enhancers	Ovary	ovary
14	chr12:75943800-75945000	Enhancers	NHDF-Ad	bronchial
15	chr12:75943800-75945000	Enhancers	NHLF	lung
16	chr12:75943800-75945200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:75943800-75945200	Enhancers	Fetal Muscle Leg	muscle
18	chr12:75943800-75945400	Enhancers	HSMM	muscle
19	chr12:75944000-75945000	Enhancers	Stomach Mucosa	stomach
20	chr12:75944200-75945200	Enhancers	Stomach Smooth Muscle	stomach
21	chr12:75944400-75945000	Enhancers	Psoas Muscle	Psoas
22	chr12:75944400-75945800	Enhancers	Fetal Stomach	stomach
23	chr12:75944400-75947400	Weak transcription	A549	lung
24	chr12:75944400-75947600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:75944600-75945000	Enhancers	Aorta	Aorta
26	chr12:75944600-75946200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:75944600-75947200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:75944600-75947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:75944600-75947200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:75944600-75947200	Weak transcription	NH-A	brain
31	chr12:75944800-75945000	Enhancers	Fetal Brain Female	brain
32	chr12:75944800-75945000	Flanking Active TSS	Fetal Heart	heart
33	chr12:75944800-75945400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr12:75944800-75945800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:75944800-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:75944800-75947400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:75944800-75948200	Weak transcription	Lung	lung
38	chr12:75944800-75948200	Weak transcription	Right Atrium	heart
39	chr12:75944800-75954000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links