Variant report

Variant	rs6694786
Chromosome Location	chr1:56077079-56077080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1039294	0.92[CEU][hapmap]
rs10493193	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493194	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493195	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206626	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs11206627	0.98[EUR][1000 genomes]
rs11206635	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206649	0.92[CEU][hapmap]
rs11801001	0.84[CEU][hapmap]
rs11805740	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116670	0.92[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117758	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12125730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12139482	0.92[CEU][hapmap];0.89[MEX][hapmap]
rs17418048	0.92[CEU][hapmap]
rs17418151	0.92[CEU][hapmap]
rs17452287	0.92[CEU][hapmap]
rs1846562	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1846563	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61566671	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6588567	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6670673	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6680818	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681925	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694680	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519540	0.92[CEU][hapmap]
rs7548272	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7549716	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550575	0.92[CEU][hapmap]
rs769970	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs769989	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6694786	DAB1	cis	parietal	SCAN
rs6694786	CPT2	cis	cerebellum	SCAN
rs6694786	GLIS1	cis	cerebellum	SCAN
rs6694786	ZYG11A	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:56074400-56077200	Weak transcription	Placenta	Placenta
3	chr1:56075400-56077400	Enhancers	Osteobl	bone
4	chr1:56075400-56080000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:56075800-56079200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:56076000-56077200	Enhancers	Fetal Lung	lung
7	chr1:56076000-56077400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:56076000-56077600	Enhancers	Ovary	ovary
9	chr1:56076000-56079400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:56076200-56077400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:56076200-56079200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:56076400-56079400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:56076600-56077400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:56077000-56077200	Enhancers	Aorta	Aorta
15	chr1:56077000-56077600	Enhancers	NHDF-Ad	bronchial

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