Variant report

Variant	rs2586394
Chromosome Location	chr1:172256829-172256830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172227773..172230310-chr1:172254726..172257439,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10911387	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11808940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12049422	0.93[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap]
rs12069167	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16844255	0.81[CHD][hapmap]
rs2586389	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586401	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586403	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586404	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586407	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586411	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586412	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757493	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2757495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757496	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850640	0.82[CHD][hapmap]
rs477289	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs479336	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6701929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7550558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425543	0.83[ASN][1000 genomes]
rs9425545	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006542	chr1:172253765-172304690	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2586394	F5	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:172251800-172257000	Weak transcription	Right Ventricle	heart
3	chr1:172253000-172257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:172254800-172257200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:172254800-172258400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:172255400-172257200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:172255400-172257600	Enhancers	NHLF	lung
8	chr1:172255400-172257800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:172255400-172257800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:172255800-172257400	Enhancers	A549	lung
11	chr1:172255800-172257800	Enhancers	Right Atrium	heart
12	chr1:172255800-172258000	Enhancers	NHDF-Ad	bronchial
13	chr1:172256200-172257000	Weak transcription	Pancreas	Pancrea
14	chr1:172256200-172257400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:172256200-172267400	Weak transcription	Left Ventricle	heart
16	chr1:172256200-172267400	Weak transcription	Psoas Muscle	Psoas
17	chr1:172256200-172290000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:172256400-172257200	Enhancers	HSMM	muscle
19	chr1:172256400-172257200	Enhancers	Osteobl	bone
20	chr1:172256400-172257400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:172256400-172258400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:172256400-172262000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:172256400-172290200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:172256600-172257000	Weak transcription	Fetal Heart	heart
25	chr1:172256600-172257600	Weak transcription	Fetal Lung	lung
26	chr1:172256600-172262000	Weak transcription	Ovary	ovary
27	chr1:172256600-172265200	Weak transcription	NH-A	brain
28	chr1:172256600-172289800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:172256800-172262200	Weak transcription	Adipose Nuclei	Adipose

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