Variant report

Variant	rs12532327
Chromosome Location	chr7:65535419-65535420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65534296..65537284-chr7:65539336..65540877,2	K562	blood:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs12530898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12531900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes]
rs12532675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs12534109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes]
rs12536292	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537407	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12538147	1.00[AFR][1000 genomes]
rs12538379	1.00[AFR][1000 genomes]
rs12538961	1.00[AFR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2279904	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes]
rs2292937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3735141	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62465483	1.00[AFR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62465545	1.00[AFR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62467387	0.90[EUR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62467436	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62467441	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62467442	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62467444	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62467450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes]
rs62470879	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470880	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470884	0.84[EUR][1000 genomes]
rs62470886	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470891	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470894	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470895	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470899	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470900	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470921	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470922	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470924	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470925	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62470938	0.85[EUR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62470944	0.90[EUR][1000 genomes]
rs62470945	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12532327	hmm32897	cis	multi-tissue	Pritchard
rs12532327	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12532327	RABGEF1	cis	lymphoblastoid	seeQTL
rs12532327	RABGEF1	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65531200-65537600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:65534600-65535800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:65534800-65535600	Enhancers	NHDF-Ad	bronchial
4	chr7:65534800-65540400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:65535000-65535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:65535000-65535600	Enhancers	NHEK	skin
7	chr7:65535000-65535800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:65535200-65535600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:65535400-65535800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:65535400-65537600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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