Variant report

Variant	rs12403850
Chromosome Location	chr1:220079381-220079382
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220049654..220055066-chr1:220079311..220085497,6	K562	blood:
2	chr1:220072364..220075393-chr1:220077961..220082079,4	K562	blood:
3	chr1:220070443..220076054-chr1:220076970..220083388,8	K562	blood:
4	chr1:220056357..220058646-chr1:220078386..220080543,2	K562	blood:
5	chr1:220078897..220080422-chr1:220101936..220103801,2	K562	blood:
6	chr1:220065741..220068828-chr1:220078028..220081073,4	K562	blood:
7	chr1:220078373..220081113-chr1:220217284..220220035,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12409848	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17552600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34672561	1.00[YRI][hapmap]
rs4846606	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7530353	0.81[AMR][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	nsv1006393	chr1:219925261-220126458	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1067840	chr1:219990803-220091941	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12403850	USH2A	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220077000-220080400	Weak transcription	HepG2	liver
2	chr1:220077400-220080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:220077400-220086800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:220077400-220088400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:220077400-220088600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:220079200-220079600	Enhancers	K562	blood
7	chr1:220079200-220080200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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Input of quick search could be:

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

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