Variant report

Variant	rs6686438
Chromosome Location	chr1:78769947-78769948
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1004435	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10489948	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873970	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873971	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162444	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162445	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162447	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162448	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162449	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162450	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162452	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162455	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804180	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11804577	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032466	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035240	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036413	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12036778	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12041099	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12072800	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12076370	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12082822	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12728306	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328443	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1328444	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1328445	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1417102	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1927779	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1952363	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35271660	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4650394	0.90[EUR][1000 genomes]
rs56729185	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674660	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67402345	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720887	1.00[JPT][hapmap]
rs7529466	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536898	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7539904	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545766	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553079	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553618	0.92[EUR][1000 genomes];0.91[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	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78767800-78770200	Enhancers	NHDF-Ad	bronchial
2	chr1:78768800-78770200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:78768800-78770400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:78768800-78770600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:78768800-78770600	Enhancers	Osteobl	bone
6	chr1:78768800-78770800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:78768800-78771000	Enhancers	NHLF	lung
8	chr1:78768800-78771200	Enhancers	Hela-S3	cervix
9	chr1:78769000-78770200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:78769000-78770200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:78769200-78770000	Enhancers	Adipose Nuclei	Adipose
12	chr1:78769200-78770000	Enhancers	HSMM	muscle
13	chr1:78769200-78770000	Enhancers	NHEK	skin
14	chr1:78769200-78770600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:78769200-78770600	Enhancers	HMEC	breast
16	chr1:78769600-78770600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:78769800-78770000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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