Variant report

Variant	rs656721
Chromosome Location	chr3:133118109-133118110
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	chr3:133116761..133118281-chr3:133121220..133123369,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1114630	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1197287	0.86[JPT][hapmap]
rs1197288	0.95[JPT][hapmap]
rs1197296	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs1197297	0.91[JPT][hapmap]
rs1197298	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1197299	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1197301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1197302	0.96[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1197304	0.89[CEU][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs1197305	0.95[JPT][hapmap]
rs1197306	0.95[JPT][hapmap]
rs1197309	0.89[CEU][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs1197311	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1197312	0.81[YRI][hapmap]
rs1197313	0.95[JPT][hapmap]
rs1197314	0.95[JPT][hapmap]
rs1201671	0.88[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1201673	0.91[JPT][hapmap]
rs12631678	0.90[JPT][hapmap]
rs1619552	0.95[JPT][hapmap]
rs1619622	0.95[JPT][hapmap]
rs1708376	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1708377	0.88[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1708385	0.91[JPT][hapmap]
rs1795107	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2089987	0.91[JPT][hapmap]
rs2670179	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2699880	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs2699882	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732572	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs4854719	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs4854720	0.91[JPT][hapmap]
rs502538	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs517255	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs553211	0.83[JPT][hapmap]
rs56181416	0.83[EUR][1000 genomes]
rs6802663	0.91[JPT][hapmap]
rs9850193	0.81[CHD][hapmap];0.91[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	nsv460857	chr3:133101390-133122216	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv591801	chr3:133101390-133122216	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133099600-133122600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:133103400-133123200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:133103400-133123600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:133103800-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:133103800-133123800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:133104000-133122200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:133104400-133131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:133107200-133123800	Weak transcription	Fetal Thymus	thymus
9	chr3:133110000-133120400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:133110200-133120400	Weak transcription	Fetal Brain Male	brain
11	chr3:133110800-133123600	Weak transcription	HSMM	muscle
12	chr3:133112600-133119400	Strong transcription	Fetal Brain Female	brain
13	chr3:133112600-133120400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:133112600-133122200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:133113200-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:133113400-133120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:133113400-133122200	Weak transcription	Fetal Lung	lung
18	chr3:133113600-133123600	Weak transcription	HSMMtube	muscle
19	chr3:133114200-133127400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:133114800-133120200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:133115800-133120200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:133116000-133120600	Weak transcription	Lung	lung
23	chr3:133116200-133120400	Weak transcription	Brain Germinal Matrix	brain
24	chr3:133117000-133119000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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