Variant report

Variant	rs1962890
Chromosome Location	chr3:159354028-159354029
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	chr3:159351342..159356372-chr3:159480280..159483892,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10154893	0.83[ASN][1000 genomes]
rs11921824	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11921827	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12107648	0.84[ASN][1000 genomes]
rs13434009	0.86[ASN][1000 genomes]
rs1343824	0.84[ASN][1000 genomes]
rs1347671	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1347672	0.91[ASN][1000 genomes]
rs1437520	0.90[ASN][1000 genomes]
rs16830519	0.83[ASN][1000 genomes]
rs16830523	0.83[ASN][1000 genomes]
rs16830534	0.85[ASN][1000 genomes]
rs16830546	0.90[ASN][1000 genomes]
rs16830575	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16830579	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16830581	0.96[ASN][1000 genomes]
rs16830589	0.92[ASN][1000 genomes]
rs1816621	0.90[ASN][1000 genomes]
rs1816622	0.85[ASN][1000 genomes]
rs1978830	0.92[ASN][1000 genomes]
rs28434644	0.99[ASN][1000 genomes]
rs28743043	0.83[ASN][1000 genomes]
rs2886621	0.92[ASN][1000 genomes]
rs4494974	0.90[ASN][1000 genomes]
rs59556163	0.84[ASN][1000 genomes]
rs61018732	0.84[ASN][1000 genomes]
rs61373569	0.84[ASN][1000 genomes]
rs6768439	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6772245	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73012253	0.85[ASN][1000 genomes]
rs750688	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290046	0.92[ASN][1000 genomes]
rs9290047	0.92[ASN][1000 genomes]
rs9809076	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9819000	0.82[ASN][1000 genomes]
rs9819080	0.85[ASN][1000 genomes]
rs9821936	0.91[EUR][1000 genomes]
rs9824363	0.84[ASN][1000 genomes]
rs9826416	0.94[EUR][1000 genomes]
rs9826417	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9829310	0.92[ASN][1000 genomes]
rs9831125	0.94[EUR][1000 genomes]
rs9832970	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9842465	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9848763	0.90[ASN][1000 genomes]
rs9848897	0.90[ASN][1000 genomes]
rs9849705	0.82[ASN][1000 genomes]
rs9851700	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857497	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9867212	1.00[ASN][1000 genomes]
rs9870872	0.85[ASN][1000 genomes]
rs9877425	0.92[ASN][1000 genomes]
rs9879792	1.00[ASN][1000 genomes]
rs9882328	0.90[ASN][1000 genomes]
rs9883498	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159350600-159358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:159353000-159355200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:159353000-159355200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:159353000-159355200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:159353000-159358000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:159353200-159354600	Weak transcription	Hela-S3	cervix
7	chr3:159353200-159354800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:159353200-159355000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:159353200-159355000	Weak transcription	HSMMtube	muscle
10	chr3:159353200-159355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:159353200-159355200	Weak transcription	HSMM	muscle
12	chr3:159353200-159355600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:159353200-159355600	Weak transcription	NHEK	skin
14	chr3:159353200-159355800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:159353200-159356000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:159353200-159356200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:159353200-159358000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:159353200-159358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:159353200-159358000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:159353200-159358200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:159353400-159354800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:159353400-159354800	Weak transcription	NHDF-Ad	bronchial
23	chr3:159353400-159355000	Weak transcription	Osteobl	bone
24	chr3:159353400-159355800	Weak transcription	HMEC	breast
25	chr3:159353600-159354800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:159353600-159355000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:159353600-159355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:159353600-159355200	Enhancers	A549	lung
29	chr3:159353600-159355200	Weak transcription	NH-A	brain
30	chr3:159353600-159355200	Weak transcription	NHLF	lung

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