Variant report

Variant	rs9375877
Chromosome Location	chr6:132690239-132690240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10499185	1.00[CEU][hapmap]
rs11966044	0.89[EUR][1000 genomes]
rs11968833	0.83[GIH][hapmap]
rs13190939	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13196312	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs1338387	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1338388	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061202	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs17792959	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1981187	0.88[EUR][1000 genomes]
rs28385615	0.93[EUR][1000 genomes]
rs34390977	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34608104	0.92[EUR][1000 genomes]
rs34807768	0.92[EUR][1000 genomes]
rs35876357	0.86[EUR][1000 genomes]
rs36085961	0.93[EUR][1000 genomes]
rs4897577	0.88[EUR][1000 genomes]
rs6914923	0.93[EUR][1000 genomes]
rs6937164	0.84[MEX][hapmap]
rs7740690	0.92[EUR][1000 genomes]
rs7761051	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs7763146	0.92[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7766544	0.82[EUR][1000 genomes]
rs9375876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385602	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs9388985	0.84[EUR][1000 genomes]
rs9388989	0.94[MEX][hapmap]
rs9493294	0.92[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886674	chr6:132613798-132694751	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv830811	chr6:132623160-132787539	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv886675	chr6:132683762-132730947	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv604668	chr6:132687248-132731358	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9375877	CTGF	cis	parietal	SCAN
rs9375877	POU4F1	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132677400-132701200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:132678600-132690400	Weak transcription	NH-A	brain
3	chr6:132682000-132692200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:132682200-132705800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:132687000-132690400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:132687400-132690400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:132688000-132692000	Weak transcription	Fetal Lung	lung
8	chr6:132688400-132692000	Weak transcription	Fetal Kidney	kidney
9	chr6:132689000-132690800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:132689600-132693600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:132690000-132690400	Genic enhancers	NHDF-Ad	bronchial
12	chr6:132690000-132690400	Enhancers	Osteobl	bone
13	chr6:132690000-132690600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:132690000-132690600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:132690200-132690600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:132690200-132690800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:132690200-132690800	Enhancers	HSMM	muscle
18	chr6:132690200-132690800	Enhancers	HSMMtube	muscle

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