Variant report

Variant	rs12036536
Chromosome Location	chr1:222152402-222152403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10863674	0.89[ASN][1000 genomes]
rs11118919	0.85[YRI][hapmap]
rs11118925	0.92[ASN][1000 genomes]
rs12035755	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17441981	0.92[ASN][1000 genomes]
rs2225999	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4475760	0.81[AFR][1000 genomes]
rs6671937	0.81[YRI][hapmap]
rs6686477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12036536	USH2A	cis	cerebellum	SCAN
rs12036536	SLC30A10	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222146200-222163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:222148800-222154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:222150800-222152600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:222152200-222152600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:222152200-222152800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:222152400-222152600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:222152400-222152600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:222152400-222152600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:222152400-222152600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:222152400-222153000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
11	chr1:222152400-222153000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:222152400-222153200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:222152400-222153200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:222152400-222156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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