Variant report

Variant	rs9388828
Chromosome Location	chr6:131001129-131001130
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1532987	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566182	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1587292	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813596	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1909075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933761	0.86[EUR][1000 genomes]
rs1933763	0.82[EUR][1000 genomes]
rs2020093	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133005	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173302	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4632915	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897448	0.81[ASN][1000 genomes]
rs5027240	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569697	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67307248	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901835	0.82[ASN][1000 genomes]
rs6909997	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6933389	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933692	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741777	0.81[ASN][1000 genomes]
rs7746694	0.91[EUR][1000 genomes]
rs7747285	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756492	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7774595	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775216	0.82[EUR][1000 genomes]
rs9321247	0.86[EUR][1000 genomes]
rs9321248	0.87[EUR][1000 genomes]
rs9372974	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372975	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372976	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375758	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388825	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388829	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388830	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388831	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402266	0.90[EUR][1000 genomes]
rs9402267	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv533971	chr6:130490694-131172051	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv427767	chr6:130875056-131008620	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830806	chr6:130938330-131107137	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr6:130993800-131005400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:130996600-131001600	Weak transcription	HUVEC	blood vessel
3	chr6:130997000-131001400	Weak transcription	NH-A	brain
4	chr6:130997600-131005400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:130998000-131002000	Weak transcription	HSMM	muscle
6	chr6:131000400-131001200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:131000600-131001400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:131000600-131001800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:131000600-131002400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:131000600-131003000	Enhancers	NHDF-Ad	bronchial
11	chr6:131000600-131003000	Enhancers	NHEK	skin
12	chr6:131000600-131003200	Enhancers	NHLF	lung
13	chr6:131000600-131003200	Enhancers	Osteobl	bone
14	chr6:131001000-131001200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:131001000-131001400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:131001000-131001400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:131001000-131001800	Enhancers	Ovary	ovary
18	chr6:131001000-131002000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:131001000-131002400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:131001000-131002400	Enhancers	HMEC	breast
21	chr6:131001000-131002600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:131001000-131003200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:131001000-131003200	Enhancers	HSMMtube	muscle

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