Variant report

Variant	rs3005890
Chromosome Location	chr1:56781630-56781631
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	chr1:56781396..56783782-chr1:56786454..56788115,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2793659	0.80[AMR][1000 genomes]
rs2994548	0.81[AMR][1000 genomes]
rs2994549	0.81[AMR][1000 genomes]
rs2994550	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994551	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994552	0.83[AMR][1000 genomes]
rs2994553	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994554	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2994555	0.81[AMR][1000 genomes]
rs2994556	0.81[AMR][1000 genomes]
rs2994557	0.80[AMR][1000 genomes]
rs2994558	0.80[AMR][1000 genomes]
rs3005885	0.80[AMR][1000 genomes]
rs3005886	0.80[AMR][1000 genomes]
rs3005887	0.80[AMR][1000 genomes]
rs3005888	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005889	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3005892	0.81[AMR][1000 genomes]
rs3005893	0.81[AMR][1000 genomes]
rs3005894	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3005895	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3005896	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005897	0.83[AMR][1000 genomes]
rs3005898	0.83[AMR][1000 genomes]
rs3005899	0.83[AMR][1000 genomes]
rs3005900	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005902	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005904	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005905	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9787000	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56757800-56786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:56768200-56791000	Weak transcription	Aorta	Aorta
4	chr1:56769600-56788000	Weak transcription	Right Atrium	heart
5	chr1:56770000-56791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:56770400-56792200	Weak transcription	Right Ventricle	heart
7	chr1:56770600-56786600	Weak transcription	Left Ventricle	heart
8	chr1:56772000-56783600	Weak transcription	Ovary	ovary
9	chr1:56776800-56784200	Weak transcription	NHDF-Ad	bronchial
10	chr1:56778000-56781800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:56780200-56785600	Weak transcription	Fetal Lung	lung
12	chr1:56780200-56786200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:56780200-56786600	Weak transcription	Psoas Muscle	Psoas
14	chr1:56780400-56793600	Weak transcription	Liver	Liver
15	chr1:56781600-56781800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:56781600-56782000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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