Variant report

Variant	rs10948787
Chromosome Location	chr6:53802307-53802308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53802203..53805380-chr6:53806061..53808380,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456674	0.91[YRI][hapmap]
rs11751301	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11759220	0.81[EUR][1000 genomes]
rs12204130	0.91[YRI][hapmap]
rs12661475	0.81[EUR][1000 genomes]
rs12661938	0.82[EUR][1000 genomes]
rs12663216	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs13437448	0.97[EUR][1000 genomes]
rs1883632	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2076496	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2076497	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3001004	0.81[EUR][1000 genomes]
rs3001005	0.81[EUR][1000 genomes]
rs3001006	0.81[EUR][1000 genomes]
rs3001007	0.81[EUR][1000 genomes]
rs3001008	0.81[EUR][1000 genomes]
rs3003488	0.81[EUR][1000 genomes]
rs3003490	0.81[EUR][1000 genomes]
rs3003492	0.93[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs3003494	0.81[EUR][1000 genomes]
rs3003498	0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap]
rs3813850	0.82[CHB][hapmap];0.91[GIH][hapmap]
rs4254992	0.81[EUR][1000 genomes]
rs4486000	0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4618525	0.81[EUR][1000 genomes]
rs4640878	0.81[EUR][1000 genomes]
rs4712050	0.98[EUR][1000 genomes]
rs4712051	0.96[EUR][1000 genomes]
rs5006063	0.97[EUR][1000 genomes]
rs61068246	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62396285	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62397076	0.81[EUR][1000 genomes]
rs62397090	0.82[EUR][1000 genomes]
rs6905323	0.82[EUR][1000 genomes]
rs6905563	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs6906326	0.82[CHB][hapmap]
rs6909040	0.80[EUR][1000 genomes]
rs6909094	0.81[EUR][1000 genomes]
rs6927232	0.97[EUR][1000 genomes]
rs763813	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs763815	0.97[EUR][1000 genomes]
rs7750173	0.86[EUR][1000 genomes]
rs9296720	0.81[EUR][1000 genomes]
rs9296727	0.97[EUR][1000 genomes]
rs9474643	0.82[CHB][hapmap]
rs9474661	0.81[EUR][1000 genomes]
rs9474665	0.81[EUR][1000 genomes]
rs9474687	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10948787	BAG2	cis	cerebellum	SCAN
rs10948787	C6orf142	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53772000-53803000	Weak transcription	Lung	lung
2	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
3	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:53794600-53807800	Weak transcription	Left Ventricle	heart
5	chr6:53794800-53803200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:53794800-53815600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53795200-53803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:53795200-53807400	Weak transcription	Fetal Stomach	stomach
9	chr6:53795600-53826200	Weak transcription	NHEK	skin
10	chr6:53795800-53803000	Weak transcription	Esophagus	oesophagus
11	chr6:53799800-53803200	Weak transcription	HSMMtube	muscle
12	chr6:53799800-53810600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:53801000-53803000	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links