Variant report

Variant	rs3005898
Chromosome Location	chr1:56787096-56787097
allele	A/G
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: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2793659	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2994548	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2994549	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2994550	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994551	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2994553	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994555	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2994556	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2994557	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2994558	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005883	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3005885	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005886	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005890	0.83[AMR][1000 genomes]
rs3005892	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005893	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005896	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3005899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005900	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005901	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3005902	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005904	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005905	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3005912	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3005913	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6588617	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6670695	0.84[EUR][1000 genomes]
rs72916227	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1015037	chr1:56784322-56814739	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56768200-56791000	Weak transcription	Aorta	Aorta
3	chr1:56769600-56788000	Weak transcription	Right Atrium	heart
4	chr1:56770000-56791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:56770400-56792200	Weak transcription	Right Ventricle	heart
6	chr1:56780400-56793600	Weak transcription	Liver	Liver
7	chr1:56781800-56791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:56784200-56788000	Enhancers	NHDF-Ad	bronchial
10	chr1:56784200-56791000	Weak transcription	Ovary	ovary
11	chr1:56784200-56792200	Weak transcription	Lung	lung
12	chr1:56785600-56787200	Enhancers	Fetal Muscle Leg	muscle
13	chr1:56785600-56787400	Enhancers	Fetal Heart	heart
14	chr1:56786400-56787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:56786600-56787400	Enhancers	Psoas Muscle	Psoas
16	chr1:56786800-56788000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:56787000-56788000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:56787000-56789800	Weak transcription	Fetal Lung	lung
19	chr1:56787000-56805600	Weak transcription	Left Ventricle	heart

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