Variant report

Variant	rs4876399
Chromosome Location	chr8:119045329-119045330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:119039290..119041869-chr8:119044899..119048314,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10088107	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10088828	0.81[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10095646	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10099230	0.81[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10104745	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10106128	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1020916	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10216949	0.89[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10505325	0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10955850	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955851	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs10955852	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs11562725	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11562727	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11562814	0.81[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1188	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12541849	0.92[ASN][1000 genomes]
rs12544344	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13264371	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs13271950	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13277304	0.85[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs13277610	0.85[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs13282822	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100617	0.92[ASN][1000 genomes]
rs2124959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6990802	0.81[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs6997001	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7004377	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73325947	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7357466	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7357586	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7357588	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7813805	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7819492	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7829981	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7832327	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7833710	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881989	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9649944	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9650073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1025002	chr8:118970940-119069418	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119036600-119046600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:119037200-119046600	Weak transcription	Brain Hippocampus Middle	brain
3	chr8:119037600-119046600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:119037600-119046600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr8:119038200-119046600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:119038400-119046400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:119038400-119046600	Weak transcription	Spleen	Spleen
8	chr8:119038400-119046800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:119038800-119046400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:119039200-119046400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:119039200-119046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:119039200-119046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:119039200-119046800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr8:119039200-119049000	Weak transcription	HUVEC	blood vessel
15	chr8:119040000-119045800	Weak transcription	Psoas Muscle	Psoas
16	chr8:119040000-119046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:119040000-119046600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr8:119040400-119046600	Weak transcription	Fetal Heart	heart
19	chr8:119040600-119052600	Weak transcription	Left Ventricle	heart
20	chr8:119041200-119046800	Enhancers	Osteobl	bone
21	chr8:119041400-119046800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:119041400-119049800	Enhancers	NHDF-Ad	bronchial
23	chr8:119041600-119045800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr8:119041800-119049800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:119042000-119045400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr8:119042200-119046800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr8:119042400-119046600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr8:119042400-119052000	Weak transcription	Adipose Nuclei	Adipose
29	chr8:119042800-119045400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr8:119043000-119045400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr8:119043000-119048400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr8:119043200-119045400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr8:119043200-119046800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:119043200-119048400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:119043200-119050800	Enhancers	HMEC	breast
36	chr8:119043400-119046800	Weak transcription	Ovary	ovary
37	chr8:119043400-119054400	Weak transcription	Colon Smooth Muscle	Colon
38	chr8:119043400-119054400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:119043600-119045800	Weak transcription	Aorta	Aorta
40	chr8:119043600-119046600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:119043600-119046600	Weak transcription	Esophagus	oesophagus
42	chr8:119043600-119046600	Weak transcription	Pancreas	Pancrea
43	chr8:119043800-119046600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr8:119043800-119046800	Weak transcription	Lung	lung
45	chr8:119044000-119045400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr8:119044200-119046400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr8:119044200-119046400	Weak transcription	HSMMtube	muscle
48	chr8:119044200-119046400	Weak transcription	NH-A	brain
49	chr8:119044200-119049000	Weak transcription	HepG2	liver
50	chr8:119044400-119046600	Weak transcription	Fetal Lung	lung

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