Variant report

Variant	rs7956673
Chromosome Location	chr12:76027975-76027976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:76001058..76002737-chr12:76026565..76029545,2	K562	blood:
2	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10748282	0.85[EUR][1000 genomes]
rs10785198	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879929	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879932	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879933	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879934	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879935	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879936	0.88[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879938	0.80[CEU][hapmap]
rs10879945	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10879949	0.99[ASN][1000 genomes]
rs11180562	0.84[EUR][1000 genomes]
rs11180575	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11180584	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11180598	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180603	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11514051	0.91[EUR][1000 genomes]
rs11519910	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11520226	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12811250	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17115238	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2054516	0.97[ASN][1000 genomes]
rs2054518	0.84[EUR][1000 genomes]
rs2366988	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2366989	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2886826	0.85[EUR][1000 genomes]
rs2886828	0.92[ASN][1000 genomes]
rs34406885	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3847671	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3898937	0.88[EUR][1000 genomes]
rs4323912	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4882631	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs4882635	0.83[ASN][1000 genomes]
rs58886425	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60465677	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6582293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582294	0.98[ASN][1000 genomes]
rs7137366	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7137610	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297580	0.97[ASN][1000 genomes]
rs7300994	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7305673	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7314159	0.82[ASN][1000 genomes]
rs7314220	0.88[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7315474	0.99[ASN][1000 genomes]
rs733881	0.80[CEU][hapmap]
rs7955264	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7956953	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958508	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7962144	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7962276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979460	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7979600	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7980713	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9634253	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7956673	GLIPR1L2	cis	Thyroid	GTEx
rs7956673	GLIPR1L2	cis	lung	GTEx
rs7956673	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs7956673	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs7956673	GLIPR1L2	cis	Nerve Tibial	GTEx
rs7956673	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs7956673	GLIPR1L2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:76018000-76028600	Weak transcription	NHLF	lung
3	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:76018400-76029400	Weak transcription	NHEK	skin
6	chr12:76023400-76028200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:76024200-76028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:76025000-76028400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:76025400-76030800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:76025600-76032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:76025800-76030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:76026200-76030200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:76026600-76028400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:76026600-76028600	Weak transcription	NH-A	brain
15	chr12:76026600-76028600	Weak transcription	NHDF-Ad	bronchial
16	chr12:76026600-76028800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:76026600-76029000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:76026600-76035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:76026800-76028200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:76027000-76028800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:76027000-76029600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:76027000-76029600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:76027400-76028000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr12:76027400-76028000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:76027400-76028000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:76027400-76029800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr12:76027400-76030000	Enhancers	Fetal Lung	lung
28	chr12:76027600-76028000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr12:76027600-76030200	Enhancers	HUVEC	blood vessel
30	chr12:76027600-76031000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:76027800-76028200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:76027800-76028200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:76027800-76031000	Enhancers	HepG2	liver

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