Variant report

Variant	rs12566616
Chromosome Location	chr1:210058735-210058736
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	chr1:210057678..210059347-chr1:210545335..210547979,2	MCF-7	breast:
2	chr1:210042123..210044687-chr1:210056362..210058775,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12561877	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12563982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565234	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12565533	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12567184	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12567185	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12569195	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28866038	0.94[ASN][1000 genomes]
rs35163211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57891047	1.00[AMR][1000 genomes]
rs72468060	1.00[AMR][1000 genomes]
rs72468062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72649911	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649922	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649926	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649927	1.00[AMR][1000 genomes]
rs72649928	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649929	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649930	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649931	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649932	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649933	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649934	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649935	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649936	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649939	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649941	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649942	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649943	1.00[AMR][1000 genomes]
rs72649944	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649945	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649946	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649947	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649950	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72649951	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9919217	0.89[EUR][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210053600-210058800	Enhancers	Brain Hippocampus Middle	brain
2	chr1:210055600-210060400	Enhancers	HSMMtube	muscle
3	chr1:210055800-210060000	Weak transcription	Pancreas	Pancrea
4	chr1:210055800-210060200	Enhancers	HSMM	muscle
5	chr1:210056200-210060400	Enhancers	NHEK	skin
6	chr1:210056400-210058800	Enhancers	HUVEC	blood vessel
7	chr1:210056400-210059000	Enhancers	NHLF	lung
8	chr1:210056400-210059400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:210056400-210059800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:210056400-210060400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:210056400-210060400	Enhancers	HMEC	breast
12	chr1:210056600-210058800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:210056600-210060000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:210056600-210060200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:210056800-210059400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:210057000-210059200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:210057200-210059800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:210057600-210058800	Enhancers	Fetal Intestine Large	intestine
19	chr1:210058000-210059200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:210058000-210059400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:210058000-210059800	Enhancers	NHDF-Ad	bronchial
22	chr1:210058000-210061200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:210058000-210064000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:210058200-210059200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:210058200-210059400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:210058200-210059800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:210058200-210060200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:210058200-210060200	Enhancers	NH-A	brain
29	chr1:210058200-210060600	Enhancers	Hela-S3	cervix
30	chr1:210058400-210059600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:210058400-210061600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:210058600-210059000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:210058600-210059200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:210058600-210060400	Enhancers	Osteobl	bone
35	chr1:210058600-210063200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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