Variant report

Variant	rs12787112
Chromosome Location	chr11:47687147-47687148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10128705	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1064608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039308	0.86[ASN][1000 genomes]
rs11039324	0.87[ASN][1000 genomes]
rs11039342	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039348	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039355	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039389	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039390	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039391	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039426	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11602339	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11602395	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604825	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605774	0.82[ASN][1000 genomes]
rs11823949	0.84[ASN][1000 genomes]
rs12361031	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12363232	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12418852	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs12419507	0.87[ASN][1000 genomes]
rs12419692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12421210	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12785833	0.82[ASN][1000 genomes]
rs12787330	0.82[ASN][1000 genomes]
rs12787646	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12798346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12799623	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12803191	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs34910028	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34923397	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34958982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs35805829	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35902101	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752797	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4752845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56400411	0.81[AMR][1000 genomes]
rs59360790	0.91[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs7120333	0.82[ASN][1000 genomes]
rs7124681	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7130758	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7928842	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12787112	C1QTNF4	cis	lung	GTEx
rs12787112	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12787112	C1QTNF4	cis	Artery Tibial	GTEx
rs12787112	C1QTNF4	cis	Whole Blood	GTEx
rs12787112	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12787112	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12787112	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12787112	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12787112	SPI1	cis	multi-tissue	Pritchard
rs12787112	Hs.6637	cis	multi-tissue	Pritchard
rs12787112	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12787112	C1QTNF4	cis	multi-tissue	Pritchard
rs12787112	FNBP4	cis	lesional skin	skin_eQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47676800-47703400	Weak transcription	Fetal Intestine Small	intestine
2	chr11:47682000-47688600	Weak transcription	HepG2	liver
3	chr11:47683200-47688200	Weak transcription	Fetal Lung	lung
4	chr11:47685600-47687200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:47685600-47688400	Weak transcription	Fetal Stomach	stomach
6	chr11:47686600-47687200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:47687000-47692600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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