Variant report

Variant	rs171224
Chromosome Location	chr6:54807006-54807007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10456176	0.86[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs10948866	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs10948879	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108887	0.84[ASN][1000 genomes]
rs1108888	0.84[ASN][1000 genomes]
rs12192659	0.88[CHB][hapmap]
rs12215464	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1354288	0.84[ASN][1000 genomes]
rs1393775	0.84[ASN][1000 genomes]
rs1393776	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1472679	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs148109	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1503134	0.82[ASN][1000 genomes]
rs1503136	0.84[ASN][1000 genomes]
rs1503140	0.84[ASN][1000 genomes]
rs1580891	0.84[ASN][1000 genomes]
rs1580892	0.84[ASN][1000 genomes]
rs181155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1910350	0.84[ASN][1000 genomes]
rs1963697	0.93[CHB][hapmap]
rs2134537	0.84[ASN][1000 genomes]
rs2134538	0.84[ASN][1000 genomes]
rs2134539	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2174115	0.84[ASN][1000 genomes]
rs2179786	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2207025	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][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]
rs2207026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239779	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239792	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239794	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs239796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs239801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239813	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239815	0.89[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs239837	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]
rs239850	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239854	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2746443	0.81[EUR][1000 genomes]
rs2816810	0.85[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2816811	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs2816812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3125261	0.83[ASN][1000 genomes]
rs3125263	0.84[ASN][1000 genomes]
rs3125267	0.84[ASN][1000 genomes]
rs3125269	0.84[ASN][1000 genomes]
rs421957	0.89[CEU][hapmap];0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs4712082	0.80[CHB][hapmap]
rs4712083	0.84[ASN][1000 genomes]
rs4715492	0.82[ASN][1000 genomes]
rs6459034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6902245	0.84[ASN][1000 genomes]
rs6902422	0.84[ASN][1000 genomes]
rs6918402	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs6922186	0.84[ASN][1000 genomes]
rs6926997	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6929930	0.84[ASN][1000 genomes]
rs6937970	0.85[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs7741915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7764641	0.82[ASN][1000 genomes]
rs7765236	0.82[ASN][1000 genomes]
rs7765721	0.85[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap]
rs931766	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs9349740	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9370345	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9382402	0.81[ASN][1000 genomes]
rs9382403	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9382404	0.82[ASN][1000 genomes]
rs9382407	0.82[ASN][1000 genomes]
rs9396011	0.82[ASN][1000 genomes]
rs9475078	0.84[ASN][1000 genomes]
rs960834	0.81[ASN][1000 genomes]
rs971526	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs973205	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs980821	0.84[ASN][1000 genomes]
rs980822	0.84[ASN][1000 genomes]
rs988913	0.93[CHB][hapmap];1.00[JPT][hapmap]

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:17 , 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	chr6:54800400-54807600	Weak transcription	Small Intestine	intestine
5	chr6:54802200-54809600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:54802600-54810800	Weak transcription	Pancreas	Pancrea
7	chr6:54804200-54807800	Strong transcription	NHEK	skin
8	chr6:54804400-54807400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:54804600-54809200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:54805200-54808200	Weak transcription	Fetal Intestine Large	intestine
11	chr6:54805400-54811400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:54805600-54807200	Weak transcription	Hela-S3	cervix
13	chr6:54805600-54807400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:54805600-54808000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:54805600-54808400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:54806600-54809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:54806800-54808400	Weak transcription	HMEC	breast

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