Variant report

Variant	rs12465795
Chromosome Location	chr2:173564638-173564639
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	chr2:173558154..173560301-chr2:173561566..173564675,4	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1010752	0.84[ASN][1000 genomes]
rs10930566	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930567	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930568	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930569	0.82[ASN][1000 genomes]
rs12052531	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465512	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12469378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617037	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12617921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620518	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621044	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13423020	0.81[ASN][1000 genomes]
rs1530864	0.80[ASN][1000 genomes]
rs1530865	0.80[ASN][1000 genomes]
rs1531148	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1531149	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860693	0.80[ASN][1000 genomes]
rs16860781	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860789	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860834	1.00[AFR][1000 genomes]
rs2122833	0.95[EUR][1000 genomes]
rs28761282	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4395226	0.81[ASN][1000 genomes]
rs59578456	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59606385	1.00[AFR][1000 genomes]
rs60127617	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61121406	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61505737	0.80[ASN][1000 genomes]
rs6433376	0.82[ASN][1000 genomes]
rs6709144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718681	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6719140	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6733671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70937083	0.80[ASN][1000 genomes]
rs70937084	0.80[ASN][1000 genomes]
rs836628	0.86[ASN][1000 genomes]
rs836643	0.95[EUR][1000 genomes];0.92[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173560600-173565400	Weak transcription	Esophagus	oesophagus
2	chr2:173563400-173565600	Weak transcription	HSMM	muscle
3	chr2:173563400-173565800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:173563400-173565800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:173563600-173565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173563600-173565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:173563600-173565600	Weak transcription	NHDF-Ad	bronchial
8	chr2:173563600-173565800	Weak transcription	Hela-S3	cervix
9	chr2:173563600-173565800	Weak transcription	HUVEC	blood vessel
10	chr2:173563600-173565800	Weak transcription	Osteobl	bone
11	chr2:173563600-173566200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:173563800-173565600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:173563800-173565600	Weak transcription	NH-A	brain
14	chr2:173563800-173566200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:173564000-173571600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:173564200-173565600	Weak transcription	HMEC	breast
17	chr2:173564200-173568000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:173564200-173575600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:173564400-173565400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:173564400-173565800	Weak transcription	A549	lung
21	chr2:173564400-173565800	Weak transcription	NHEK	skin
22	chr2:173564400-173565800	Weak transcription	NHLF	lung
23	chr2:173564600-173565400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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