Variant report

Variant	rs239837
Chromosome Location	chr6:54768159-54768160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456176	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs10948866	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs10948879	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192659	0.87[CHB][hapmap]
rs12208341	0.81[AMR][1000 genomes]
rs12208348	0.81[AMR][1000 genomes]
rs1393776	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1472679	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs148109	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs171224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs181155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963697	0.93[CHB][hapmap]
rs2134539	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2179786	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2207025	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2207026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239779	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs239781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239792	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239794	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs239796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239813	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239815	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs239850	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs239854	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2746443	0.82[EUR][1000 genomes]
rs2816810	0.84[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2816811	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2816812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3996950	0.80[EUR][1000 genomes]
rs4141552	0.83[CHD][hapmap]
rs421957	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6459034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6918402	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs6926997	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6937970	0.84[CEU][hapmap];0.87[CHB][hapmap]
rs7741915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs7765721	0.83[CEU][hapmap];0.93[CHB][hapmap]
rs931766	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs9349740	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9370345	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9382403	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs971526	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs973205	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs988913	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:54762000-54769000	Weak transcription	Stomach Mucosa	stomach
4	chr6:54762000-54775000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:54762200-54775000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:54763200-54768200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54763600-54768600	Weak transcription	HMEC	breast
8	chr6:54763600-54775000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:54764800-54768600	Weak transcription	NHEK	skin
10	chr6:54765600-54774400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:54765800-54780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:54766800-54771600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links