Variant report

Variant	rs1499667
Chromosome Location	chr1:56077813-56077814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10789007	0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888937	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1118219	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1118220	0.97[EUR][1000 genomes]
rs11206640	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11206643	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11206644	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1155836	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1165465	0.97[EUR][1000 genomes]
rs1165466	0.97[EUR][1000 genomes]
rs1165467	0.97[EUR][1000 genomes]
rs12085101	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12406907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499661	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1499662	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1499666	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546245	0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2047543	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2221140	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709396	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs769981	0.95[EUR][1000 genomes]
rs769982	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs769983	0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1499667	C8A	cis	parietal	SCAN

Chromatin state (count:13 , 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	chr1:56075400-56080000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:56075800-56079200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:56076000-56079400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:56076200-56079200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:56076400-56079400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:56077200-56079800	Weak transcription	Fetal Lung	lung
8	chr1:56077200-56086000	Weak transcription	Aorta	Aorta
9	chr1:56077400-56078400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:56077400-56078600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:56077400-56081400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:56077600-56078000	Weak transcription	NHDF-Ad	bronchial
13	chr1:56077800-56079600	Enhancers	Osteobl	bone

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