Variant report

Variant	rs11180603
Chromosome Location	chr12:76018778-76018779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
2	chr12:76017499..76019528-chr12:76384312..76386033,2	MCF-7	breast:
3	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
4	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:
5	chr12:76017185..76019394-chr12:76337259..76339909,2	MCF-7	breast:
6	chr12:76017340..76020194-chr12:76022357..76024091,3	MCF-7	breast:

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

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10748282	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10748283	0.81[EUR][1000 genomes]
rs10785198	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785199	0.80[EUR][1000 genomes]
rs10785200	0.80[EUR][1000 genomes]
rs10879929	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879932	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879933	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879934	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879935	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879936	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879937	0.81[EUR][1000 genomes]
rs10879938	0.81[EUR][1000 genomes]
rs10879949	0.88[ASN][1000 genomes]
rs11180562	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180575	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11180584	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180598	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11495681	0.81[EUR][1000 genomes]
rs11514051	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11519910	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11520226	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12811250	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480005	0.81[EUR][1000 genomes]
rs17115238	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2054516	0.86[ASN][1000 genomes]
rs2054518	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2366988	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2366989	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2886826	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2886828	0.81[ASN][1000 genomes]
rs34406885	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3847671	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3898937	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4323912	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4882631	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4882635	0.85[ASN][1000 genomes]
rs58886425	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60465677	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6582293	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582294	0.90[ASN][1000 genomes]
rs7137610	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297580	0.86[ASN][1000 genomes]
rs7300994	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7305673	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314159	0.84[ASN][1000 genomes]
rs7314220	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7315474	0.90[ASN][1000 genomes]
rs7955264	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956673	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7956953	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7958508	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962144	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962276	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979460	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979600	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980713	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9634253	0.87[AMR][1000 genomes];0.91[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11180603	GLIPR1L2	cis	Thyroid	GTEx
rs11180603	GLIPR1L2	cis	lung	GTEx
rs11180603	GLIPR1L2	cis	Nerve Tibial	GTEx
rs11180603	GLIPR1L2	cis	Artery Tibial	GTEx
rs11180603	RP11-585P4.5	cis	Artery Tibial	GTEx
rs11180603	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs11180603	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs11180603	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs11180603	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs11180603	RP11-585P4.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76016800-76020800	Weak transcription	K562	blood
2	chr12:76017400-76018800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:76017600-76025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:76017800-76021400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:76017800-76021400	Weak transcription	Pancreas	Pancrea
6	chr12:76017800-76022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:76018000-76025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:76018000-76025400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:76018000-76028600	Weak transcription	NHLF	lung
11	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:76018400-76020600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:76018400-76022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:76018400-76025000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:76018400-76025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:76018400-76027600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:76018400-76029400	Weak transcription	NHEK	skin
19	chr12:76018600-76021800	Weak transcription	HepG2	liver
20	chr12:76018600-76024000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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