Variant report

Variant	rs7966751
Chromosome Location	chr12:75870292-75870293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10450780	0.91[ASN][1000 genomes]
rs10879908	0.85[ASN][1000 genomes]
rs10879909	0.85[ASN][1000 genomes]
rs10879910	0.89[ASN][1000 genomes]
rs10879912	0.89[ASN][1000 genomes]
rs10879917	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11180481	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180491	0.85[ASN][1000 genomes]
rs11180502	0.84[ASN][1000 genomes]
rs11180503	0.87[ASN][1000 genomes]
rs12366783	0.81[ASN][1000 genomes]
rs12369849	0.85[ASN][1000 genomes]
rs1275478	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1275480	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1275481	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs12830818	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1480004	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1604382	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679378	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1697750	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1697752	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1697754	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697756	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1697757	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1795744	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1824980	0.88[EUR][1000 genomes]
rs1875468	0.94[ASN][1000 genomes]
rs2036387	0.93[ASN][1000 genomes]
rs2173919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704766	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2704767	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3952732	0.89[ASN][1000 genomes]
rs4019365	0.93[ASN][1000 genomes]
rs4391857	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4393363	0.82[ASN][1000 genomes]
rs4479027	0.91[ASN][1000 genomes]
rs4565938	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882621	0.85[ASN][1000 genomes]
rs4882622	0.84[ASN][1000 genomes]
rs6582290	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7135340	0.85[ASN][1000 genomes]
rs7294749	0.93[ASN][1000 genomes]
rs7295336	0.81[ASN][1000 genomes]
rs7296471	0.90[ASN][1000 genomes]
rs7300308	0.90[ASN][1000 genomes]
rs7310735	0.82[ASN][1000 genomes]
rs7971504	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[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	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7966751	GLIPR1L2	cis	cerebellum	SCAN
rs7966751	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs7966751	GLIPR1L2	cis	Nerve Tibial	GTEx
rs7966751	GLIPR1	cis	normal skin	skin_eQTL
rs7966751	RP11-585P4.5	cis	Artery Tibial	GTEx
rs7966751	GLIPR1L2	cis	Thyroid	GTEx
rs7966751	GLIPR1L2	cis	lung	GTEx
rs7966751	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs7966751	GLIPR1L2	cis	parietal	SCAN
rs7966751	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs7966751	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs7966751	GLIPR1L2	cis	Artery Tibial	GTEx
rs7966751	GLIPR1	cis	cerebellum	SCAN
rs7966751	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75865400-75874800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:75866600-75871800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:75866600-75873400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:75867000-75870600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:75868000-75870800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:75868200-75871000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:75868400-75874400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:75868400-75875600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:75868600-75873000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:75868600-75874000	Weak transcription	NHEK	skin
11	chr12:75868600-75874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:75868800-75872000	Weak transcription	HMEC	breast
13	chr12:75868800-75873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:75869000-75870400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:75869800-75871800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:75869800-75871800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:75870000-75871600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr12:75870000-75871800	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:75870000-75872000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:75870200-75872600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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