Variant report

Variant	rs6475227
Chromosome Location	chr9:18538877-18538878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10732338	0.82[EUR][1000 genomes]
rs10756978	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10810975	0.88[CHD][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10963623	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10963629	0.82[ASN][1000 genomes]
rs10963630	0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10963636	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10963642	0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12336626	0.87[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13300724	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13301259	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1341058	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1341059	0.83[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs1341060	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1341061	0.81[TSI][hapmap]
rs1361534	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1417641	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1928534	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1934931	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2383074	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2383075	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4961657	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4961658	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6475225	0.91[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7018651	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7019410	0.83[EUR][1000 genomes]
rs7027141	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7028087	0.81[EUR][1000 genomes]
rs7036067	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041523	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7044243	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7390426	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7863071	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7867817	0.93[ASN][1000 genomes]
rs7872574	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9792478	0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv892690	chr9:18485434-18592374	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv428536	chr9:18512807-18667760	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6475227	SLC24A2	cis	parietal	SCAN
rs6475227	CDKN2A	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18533200-18541200	Strong transcription	Osteobl	bone
2	chr9:18535000-18542400	Weak transcription	NHLF	lung
3	chr9:18535000-18542600	Weak transcription	Fetal Stomach	stomach
4	chr9:18535800-18540200	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr9:18535800-18541000	Strong transcription	NHDF-Ad	bronchial
6	chr9:18535800-18541200	Strong transcription	NH-A	brain
7	chr9:18536000-18542200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:18536000-18542200	Strong transcription	HSMM	muscle
9	chr9:18536200-18539000	Weak transcription	Fetal Heart	heart
10	chr9:18536200-18542800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:18536800-18542400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:18538000-18543400	Weak transcription	HSMMtube	muscle
13	chr9:18538400-18542400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:18538800-18543800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links