Variant report

Variant	rs620727
Chromosome Location	chr3:109646488-109646489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs2693621	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2693634	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2700237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950151	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950152	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34825682	0.92[ASN][1000 genomes]
rs591010	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593904	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs595732	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs598795	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs598837	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599684	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600581	0.97[ASN][1000 genomes]
rs600604	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs601036	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs604088	0.99[ASN][1000 genomes]
rs605795	0.85[ASN][1000 genomes]
rs607043	0.89[ASN][1000 genomes]
rs610419	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614845	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs617480	1.00[ASN][1000 genomes]
rs619279	0.85[ASN][1000 genomes]
rs636972	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs642142	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649118	0.86[ASN][1000 genomes]
rs652762	0.83[ASN][1000 genomes]
rs653349	0.82[ASN][1000 genomes]
rs656615	0.86[ASN][1000 genomes]
rs662181	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666016	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667006	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs671520	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686100	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686471	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs686694	0.85[ASN][1000 genomes]
rs687239	0.85[ASN][1000 genomes]
rs687619	0.85[ASN][1000 genomes]
rs687962	0.97[ASN][1000 genomes]
rs688898	0.89[ASN][1000 genomes]
rs689213	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009075	chr3:109462019-109800029	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591270	chr3:109462400-109793785	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1009550	chr3:109577315-109795453	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1839660	chr3:109591203-109678542	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv829666	chr3:109593745-109768652	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2754434	chr3:109604310-109777310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv236806	chr3:109638554-109647641	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv963568	chr3:109644954-109655353	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109641600-109646600	Weak transcription	HSMM	muscle
2	chr3:109643000-109646800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:109644000-109646800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:109645200-109647000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:109645200-109647000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:109645200-109647200	Enhancers	NH-A	brain
7	chr3:109645200-109647400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:109645200-109647400	Enhancers	HMEC	breast
9	chr3:109645400-109646600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:109645400-109647000	Enhancers	Osteobl	bone
11	chr3:109645400-109647200	Enhancers	NHEK	skin
12	chr3:109645600-109646600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:109645600-109647000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:109645600-109647000	Enhancers	Hela-S3	cervix
15	chr3:109645600-109647400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:109645800-109646800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:109645800-109646800	Enhancers	NHLF	lung
18	chr3:109645800-109647200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:109645800-109647200	Enhancers	NHDF-Ad	bronchial
20	chr3:109646000-109646800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:109646000-109647000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:109646200-109646600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:109646200-109647000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:109646400-109647000	Flanking Active TSS	A549	lung

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