Variant report

Variant	rs2757493
Chromosome Location	chr1:172267419-172267420
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	chr1:172261558..172263643-chr1:172263765..172267506,3	MCF-7	breast:
2	chr1:172262678..172264424-chr1:172266629..172268521,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10911387	0.92[ASN][1000 genomes]
rs11585706	0.81[EUR][1000 genomes]
rs11808940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs12034440	0.86[EUR][1000 genomes]
rs12039027	0.81[EUR][1000 genomes]
rs12049422	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs12069167	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844255	0.85[CHD][hapmap]
rs2421994	0.83[CHD][hapmap]
rs2586389	0.94[ASN][1000 genomes]
rs2586392	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]
rs2586394	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]
rs2586401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757496	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850640	0.80[CHD][hapmap]
rs477289	0.93[CEU][hapmap]
rs479336	0.93[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6701929	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550558	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs9425543	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425545	0.86[EUR][1000 genomes];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

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172256200-172290000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:172256400-172290200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172256600-172289800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:172260600-172271000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:172267400-172267600	ZNF genes & repeats	Left Ventricle	heart
6	chr1:172267400-172267600	Enhancers	Psoas Muscle	Psoas
7	chr1:172267400-172267600	Enhancers	GM12878-XiMat	blood
8	chr1:172267400-172267600	Enhancers	HSMM	muscle
9	chr1:172267400-172267800	Enhancers	Pancreas	Pancrea
10	chr1:172267400-172267800	Enhancers	HSMMtube	muscle
11	chr1:172267400-172268400	Enhancers	Fetal Muscle Leg	muscle

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