Variant report

Variant	rs59578456
Chromosome Location	chr2:173557204-173557205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
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	0.89[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465512	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12465795	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469378	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617037	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12617921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618078	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618132	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620518	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621044	0.81[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	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860789	0.89[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	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4395226	0.81[ASN][1000 genomes]
rs59606385	1.00[AFR][1000 genomes]
rs60127617	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61121406	0.89[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];0.97[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];0.97[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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv274888	chr2:173550156-173559068	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 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	chr2:173549800-173557400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:173552000-173557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:173556600-173559000	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr2:173556800-173559400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:173556800-173564600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:173557200-173557600	Enhancers	A549	lung
7	chr2:173557200-173557600	Enhancers	Hela-S3	cervix
8	chr2:173557200-173557800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:173557200-173557800	Enhancers	Right Ventricle	heart
10	chr2:173557200-173558000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:173557200-173558000	Enhancers	Primary T cells from cord blood	blood
12	chr2:173557200-173558000	Enhancers	NHEK	skin
13	chr2:173557200-173558200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:173557200-173558200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:173557200-173559000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:173557200-173559000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:173557200-173559000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:173557200-173559000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:173557200-173559000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:173557200-173559000	Enhancers	HMEC	breast
21	chr2:173557200-173559200	Enhancers	Fetal Heart	heart
22	chr2:173557200-173559400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:173557200-173559400	Enhancers	NHDF-Ad	bronchial
24	chr2:173557200-173559400	Enhancers	NHLF	lung

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