Variant report

Variant	rs4263159
Chromosome Location	chr2:99456151-99456152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99341666..99344183-chr2:99455107..99457899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169003	0.91[EUR][1000 genomes]
rs10172158	0.88[EUR][1000 genomes]
rs10181972	0.91[EUR][1000 genomes]
rs10188156	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123755	0.88[EUR][1000 genomes]
rs11887536	0.88[EUR][1000 genomes]
rs11893888	0.82[EUR][1000 genomes]
rs12468024	0.88[EUR][1000 genomes]
rs12712033	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12712034	0.85[CHB][hapmap]
rs12712035	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712036	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs12712038	0.88[EUR][1000 genomes]
rs12712039	0.86[EUR][1000 genomes]
rs12992214	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004923	0.91[EUR][1000 genomes]
rs13389386	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1356424	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1568213	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1581250	0.91[EUR][1000 genomes]
rs1581251	0.88[EUR][1000 genomes]
rs1878585	0.91[EUR][1000 genomes]
rs1983352	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276604	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2280256	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4850888	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851162	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851163	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851167	0.88[EUR][1000 genomes]
rs4851170	0.88[EUR][1000 genomes]
rs4851171	0.87[EUR][1000 genomes]
rs6542838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542839	0.96[CEU][hapmap];0.80[CHB][hapmap];0.93[EUR][1000 genomes]
rs6711022	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713991	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6714243	0.88[EUR][1000 genomes]
rs6717372	0.85[EUR][1000 genomes]
rs6719634	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs6726156	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6733011	0.97[ASN][1000 genomes]
rs6757099	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579189	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7581128	0.81[JPT][hapmap]
rs7608889	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs925887	0.80[EUR][1000 genomes]
rs981601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981602	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:99450600-99456200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:99450800-99462800	Weak transcription	Gastric	stomach
6	chr2:99451000-99456400	Weak transcription	Lung	lung
7	chr2:99453200-99457000	Weak transcription	Esophagus	oesophagus
8	chr2:99453200-99460600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:99454000-99456400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:99454000-99456400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:99454200-99459000	Weak transcription	A549	lung
13	chr2:99455200-99456200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:99455200-99456200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:99455200-99456200	Enhancers	HMEC	breast
16	chr2:99455600-99456200	Enhancers	NHEK	skin
17	chr2:99455800-99456200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:99456000-99456400	Enhancers	HSMM	muscle

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