Variant report

Variant	rs2871476
Chromosome Location	chr4:30867283-30867284
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	chr4:30860982..30862636-chr4:30867110..30869327,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10000401	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10013694	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10021544	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs10517219	1.00[YRI][hapmap]
rs10805300	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10939317	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10939318	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10939325	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs11727594	0.81[EUR][1000 genomes]
rs11735048	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12512796	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13120686	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13127450	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13138590	1.00[YRI][hapmap]
rs13151051	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1447365	0.85[EUR][1000 genomes]
rs28670870	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775331	1.00[YRI][hapmap]
rs4075130	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4235012	0.94[ASN][1000 genomes]
rs4235013	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4235014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4235015	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4259023	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4260492	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4261943	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4266255	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4337695	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4358358	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4361347	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs4368569	1.00[YRI][hapmap]
rs4374588	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4380481	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4466008	1.00[YRI][hapmap]
rs4469028	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4487300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4491979	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4557225	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4585258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611883	1.00[YRI][hapmap]
rs4692107	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4692109	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs4692490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5001866	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6448726	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448730	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs6812005	1.00[YRI][hapmap]
rs6840698	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6847642	1.00[YRI][hapmap]
rs7658077	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7661924	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7662881	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7669015	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7673048	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7678386	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7683848	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7683968	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7696462	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9291553	1.00[YRI][hapmap]
rs9685207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9997529	1.00[YRI][hapmap]
rs9999771	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv878810	chr4:30823157-30987395	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:30849200-30872200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:30855200-30879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:30855600-30867400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:30856200-30868600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:30857200-30868200	Weak transcription	Aorta	Aorta
6	chr4:30861800-30868000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:30862600-30867400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:30862800-30870600	Enhancers	Colon Smooth Muscle	Colon
9	chr4:30863000-30868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:30863200-30867800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:30863600-30868600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:30864200-30870000	Enhancers	Rectal Smooth Muscle	rectum
13	chr4:30864400-30868000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:30864800-30870800	Enhancers	Fetal Heart	heart
15	chr4:30865200-30867400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:30865200-30867400	Weak transcription	Fetal Stomach	stomach
17	chr4:30865200-30867400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:30865200-30868000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:30865200-30869200	Weak transcription	Ovary	ovary
20	chr4:30865200-30870400	Weak transcription	Fetal Brain Male	brain
21	chr4:30865200-30872200	Weak transcription	Left Ventricle	heart
22	chr4:30865400-30868200	Weak transcription	NHEK	skin
23	chr4:30865600-30867400	Weak transcription	NH-A	brain
24	chr4:30865600-30868000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:30865600-30868000	Weak transcription	HMEC	breast
26	chr4:30865600-30868400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:30865600-30868400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:30865800-30868200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:30866400-30867800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:30867200-30868600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:30867200-30870800	Enhancers	Fetal Lung	lung

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