Variant report

Variant	rs58086880
Chromosome Location	chr3:53711642-53711643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53711180..53712168-chr3:53743924..53744920,6	MCF-7	breast:
2	chr3:53700440..53702831-chr3:53710222..53712818,2	K562	blood:
3	chr3:53711186..53712122-chr3:53743953..53744837,3	MCF-7	breast:
4	chr3:53379336..53381314-chr3:53710176..53712329,2	K562	blood:
5	chr3:53711493..53712139-chr3:53742078..53742918,2	MCF-7	breast:
6	chr3:53711176..53712103-chr3:53722644..53723331,2	MCF-7	breast:
7	chr3:53708590..53712002-chr3:53712853..53715298,3	MCF-7	breast:
8	chr3:53705945..53708129-chr3:53709711..53711727,3	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11130377	0.87[EUR][1000 genomes]
rs11711045	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711142	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715072	0.86[EUR][1000 genomes]
rs11720002	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11925053	0.85[EUR][1000 genomes]
rs1460118	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17238364	0.93[EUR][1000 genomes]
rs1870564	0.85[EUR][1000 genomes]
rs60529666	0.88[EUR][1000 genomes]
rs6780648	0.88[EUR][1000 genomes]
rs6809164	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs898411	0.85[EUR][1000 genomes]
rs898418	0.88[ASN][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53698000-53714000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:53708200-53713600	Weak transcription	Fetal Brain Female	brain
4	chr3:53708400-53711800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53709000-53714000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53709400-53713800	Weak transcription	Fetal Brain Male	brain
7	chr3:53710200-53711800	Strong transcription	Fetal Lung	lung
8	chr3:53710200-53714000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:53710800-53713200	Weak transcription	Fetal Intestine Large	intestine
10	chr3:53711000-53711800	Enhancers	Fetal Heart	heart
11	chr3:53711200-53711800	Enhancers	Right Atrium	heart
12	chr3:53711200-53711800	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr3:53711200-53714000	Weak transcription	Fetal Kidney	kidney
14	chr3:53711400-53711800	Weak transcription	Lung	lung
15	chr3:53711600-53713800	Weak transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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