Variant report

Variant	rs16892194
Chromosome Location	chr6:39483139-39483140
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	chr6:39383062..39385072-chr6:39481069..39483184,2	K562	blood:
2	chr6:39481932..39484239-chr6:39485790..39487293,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10484823	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10947815	0.92[CEU][hapmap]
rs11751847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752438	0.82[ASN][1000 genomes]
rs11754807	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11754808	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755434	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757080	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758868	1.00[CEU][hapmap]
rs11759743	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528130	1.00[CEU][hapmap];1.00[CHB][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]
rs13200342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209820	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs13213322	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213488	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536700	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34081723	0.96[EUR][1000 genomes]
rs34720944	0.98[EUR][1000 genomes]
rs35516457	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714258	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4714261	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs55749620	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56713174	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56951565	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6458116	1.00[JPT][hapmap]
rs6458119	0.94[EUR][1000 genomes]
rs6901155	0.89[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6905995	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6913556	0.96[EUR][1000 genomes]
rs6927837	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928195	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942056	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571377	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732127	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73732138	0.97[EUR][1000 genomes]
rs73732153	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7751353	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs7751706	0.94[EUR][1000 genomes]
rs7751942	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754249	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771470	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774528	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296301	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9380876	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9471105	1.00[JPT][hapmap]
rs9471123	1.00[CEU][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9471124	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9471129	1.00[CEU][hapmap];0.94[EUR][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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16892194	C6orf226	cis	parietal	SCAN
rs16892194	CRIP3	cis	cerebellum	SCAN
rs16892194	BRPF3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39476600-39483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:39476600-39486000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:39481200-39489800	Weak transcription	Pancreas	Pancrea
4	chr6:39481400-39485200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:39481600-39485400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:39482400-39483600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:39483000-39483600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:39483000-39483600	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links