Variant report

Variant	rs2586392
Chromosome Location	chr1:172254193-172254194
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	chr1:172253395..172255527-chr1:172290385..172292894,2	MCF-7	breast:
2	chr1:172250146..172252710-chr1:172254053..172256076,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10911387	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11808940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049422	0.93[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs12069167	0.97[ASN][1000 genomes]
rs16844255	0.82[CHD][hapmap]
rs2586389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586394	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	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586403	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586404	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586407	0.97[ASN][1000 genomes]
rs2586408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2586410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2586411	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2586412	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2586413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2757493	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.97[ASN][1000 genomes]
rs2757495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2757496	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3850639	0.80[AMR][1000 genomes]
rs3850640	0.82[CHD][hapmap]
rs3895277	0.80[AMR][1000 genomes]
rs477289	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs479336	1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6701929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425543	0.81[ASN][1000 genomes]
rs9425545	0.83[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
rs2586392	F5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:172247800-172255800	Weak transcription	Left Ventricle	heart
3	chr1:172247800-172256000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172248200-172255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:172248200-172255400	Weak transcription	HSMM	muscle
6	chr1:172248200-172255400	Weak transcription	NHLF	lung
7	chr1:172248200-172255800	Weak transcription	Aorta	Aorta
8	chr1:172249200-172255400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:172249200-172255600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:172249400-172256000	Weak transcription	Esophagus	oesophagus
11	chr1:172249600-172255000	Weak transcription	NHDF-Ad	bronchial
12	chr1:172251800-172257000	Weak transcription	Right Ventricle	heart
13	chr1:172253000-172257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:172253600-172254200	Enhancers	Colon Smooth Muscle	Colon
15	chr1:172253600-172254800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:172253800-172254800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:172253800-172255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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