Variant report

Variant	rs10879900
Chromosome Location	chr12:75710004-75710005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10506668	0.82[JPT][hapmap]
rs10879902	0.88[CHB][hapmap]
rs10879903	0.87[CHB][hapmap]
rs11180441	0.83[JPT][hapmap]
rs11180455	0.81[CEU][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes]
rs11180456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180458	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180460	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11180465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11180474	0.87[CHB][hapmap]
rs11180475	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180483	0.82[JPT][hapmap]
rs11520223	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610111	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610112	0.81[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11831200	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs11837697	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12366348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12367329	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12368429	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12369556	0.82[JPT][hapmap]
rs12369854	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372516	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12581394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581416	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3087687	0.88[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4394867	0.82[JPT][hapmap]
rs4565940	0.82[JPT][hapmap]
rs4623941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882616	0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4882618	0.82[JPT][hapmap]
rs4882687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4882689	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60971359	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298343	0.84[CEU][hapmap]
rs73191008	0.84[AMR][1000 genomes]
rs73364090	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73364096	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954879	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967619	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970188	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	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	nsv520424	chr12:75646788-75740883	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv526556	chr12:75653281-75740883	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv899309	chr12:75664655-75712662	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv899311	chr12:75692261-75712662	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs10879900	GLIPR1L2	cis	Artery Aorta	GTEx
rs10879900	GLIPR1L2	cis	Nerve Tibial	GTEx
rs10879900	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs10879900	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs10879900	GLIPR1L2	cis	lung	GTEx
rs10879900	GLIPR1L1	cis	multi-tissue	Pritchard
rs10879900	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs10879900	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs10879900	GLIPR1L2	cis	Stomach	GTEx
rs10879900	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs10879900	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs10879900	GLIPR1L2	cis	Artery Tibial	GTEx
rs10879900	RP11-585P4.5	cis	Artery Tibial	GTEx
rs10879900	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs10879900	RP11-585P4.5	cis	Thyroid	GTEx
rs10879900	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs10879900	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs10879900	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs10879900	GLIPR1L2	cis	Thyroid	GTEx
rs10879900	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs10879900	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75681200-75711400	Weak transcription	Psoas Muscle	Psoas
2	chr12:75698000-75714000	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:75700000-75723000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:75700000-75723400	Weak transcription	Ovary	ovary
5	chr12:75706200-75723400	Weak transcription	Left Ventricle	heart
6	chr12:75708200-75710200	Enhancers	HSMM	muscle
7	chr12:75708400-75710200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:75708400-75710200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:75708400-75710200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:75708400-75710200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:75708400-75710200	Enhancers	NH-A	brain
12	chr12:75708400-75710200	Enhancers	NHLF	lung
13	chr12:75708400-75710400	Enhancers	NHDF-Ad	bronchial
14	chr12:75708400-75710400	Enhancers	Osteobl	bone
15	chr12:75709400-75723600	Weak transcription	HSMMtube	muscle
16	chr12:75709800-75710400	Enhancers	A549	lung
17	chr12:75710000-75710200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links