Variant report

Variant	rs9475078
Chromosome Location	chr6:54809589-54809590
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM83B-1	chr6:54807965-54809897	ENSG00000261116.1

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10456176	0.87[CHB][hapmap]
rs10485136	0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs10948866	0.87[CHB][hapmap]
rs10948879	0.82[ASN][1000 genomes]
rs1108887	0.95[ASN][1000 genomes]
rs1108888	0.95[ASN][1000 genomes]
rs1115159	0.82[CHB][hapmap]
rs1155749	0.87[CHB][hapmap]
rs12192659	0.87[CHB][hapmap]
rs12525787	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12662124	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1354288	0.95[ASN][1000 genomes]
rs1393775	0.95[ASN][1000 genomes]
rs1393776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472679	0.87[CHB][hapmap]
rs148109	0.81[CHB][hapmap]
rs1503134	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1503136	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1503140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503146	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1503147	0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1566723	0.80[EUR][1000 genomes]
rs1580891	0.95[ASN][1000 genomes]
rs1580892	0.95[ASN][1000 genomes]
rs171224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs181155	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1910350	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1963697	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064432	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2134537	0.95[ASN][1000 genomes]
rs2134538	0.95[ASN][1000 genomes]
rs2174115	0.95[ASN][1000 genomes]
rs2179786	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2207025	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2207026	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs239781	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs239783	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs239790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs239792	0.84[ASN][1000 genomes]
rs239796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs239801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs239813	0.84[ASN][1000 genomes]
rs239815	0.81[JPT][hapmap]
rs239837	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2816810	0.82[JPT][hapmap]
rs2816811	0.82[CHB][hapmap]
rs2816812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3125261	0.94[ASN][1000 genomes]
rs3125263	0.95[ASN][1000 genomes]
rs3125267	0.95[ASN][1000 genomes]
rs3125269	0.95[ASN][1000 genomes]
rs4141552	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4712081	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs4712082	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs4712083	0.95[ASN][1000 genomes]
rs4715492	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6459034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6459035	0.87[EUR][1000 genomes]
rs6902245	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902422	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908170	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6918402	0.87[CHB][hapmap]
rs6922186	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929930	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937970	0.87[CHB][hapmap]
rs6939778	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72645372	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7453866	0.82[CHB][hapmap]
rs7741915	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7744592	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7746374	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7761336	0.87[CHB][hapmap]
rs7764641	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765236	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765721	0.93[CHB][hapmap]
rs924712	0.87[CHB][hapmap]
rs9296771	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs931766	0.87[CHB][hapmap]
rs932452	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9349740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357822	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9367597	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370344	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382396	0.86[EUR][1000 genomes]
rs9382397	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382398	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382402	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382404	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382407	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382408	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396006	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9396007	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9396011	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475068	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9475069	0.83[EUR][1000 genomes]
rs9475081	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs960834	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs960835	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs971526	0.87[CHB][hapmap]
rs973205	0.87[CHB][hapmap]
rs980821	0.95[ASN][1000 genomes]
rs980822	0.95[ASN][1000 genomes]
rs988913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54789800-54810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:54797000-54811800	Weak transcription	Esophagus	oesophagus
3	chr6:54798800-54815600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:54802200-54809600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:54802600-54810800	Weak transcription	Pancreas	Pancrea
6	chr6:54805400-54811400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:54807400-54818000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:54807800-54815200	Weak transcription	NHEK	skin
9	chr6:54809200-54811800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:54809400-54817600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links