Variant report

Variant	rs1620838
Chromosome Location	chr3:101648610-101648611
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101642851..101646450-chr3:101646744..101649155,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1611792	0.82[AMR][1000 genomes]
rs1615244	0.82[AMR][1000 genomes]
rs1616007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1622608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672375	0.80[AMR][1000 genomes]
rs1672394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707601	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1707602	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707616	0.81[AMR][1000 genomes]
rs1707617	0.82[AMR][1000 genomes]
rs2203234	0.80[AMR][1000 genomes]
rs2203235	0.80[AMR][1000 genomes]
rs2221909	0.80[AMR][1000 genomes]
rs2942715	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2951449	0.80[AMR][1000 genomes]
rs67778216	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs771576	0.82[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101643600-101649200	Enhancers	Muscle Satellite Cultured Cells	--
2	chr3:101643600-101654000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:101643800-101658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:101644000-101654400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:101644400-101648800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:101644400-101651600	Weak transcription	Esophagus	oesophagus
7	chr3:101644600-101652800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:101644800-101654000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:101645800-101650800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:101647600-101648800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:101647600-101648800	Enhancers	HSMMtube	muscle
12	chr3:101647600-101649000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:101647600-101649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:101647600-101649000	Enhancers	HSMM	muscle
15	chr3:101648000-101648800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:101648200-101655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:101648400-101648800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:101648400-101650000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:101648400-101651200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:101648400-101654400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:101648400-101655000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:101648400-101655400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:101648400-101655600	Weak transcription	NHLF	lung
24	chr3:101648600-101648800	Enhancers	Fetal Muscle Leg	muscle
25	chr3:101648600-101651600	Weak transcription	NHDF-Ad	bronchial
26	chr3:101648600-101654800	Weak transcription	Osteobl	bone
27	chr3:101648600-101655600	Weak transcription	Hela-S3	cervix

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