Variant report

Variant	rs12562188
Chromosome Location	chr1:222040530-222040531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495181	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10779461	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11118876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118877	0.88[ASN][1000 genomes]
rs11118878	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118879	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11118882	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11583667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586814	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12027640	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047353	0.88[ASN][1000 genomes]
rs12140184	0.88[ASN][1000 genomes]
rs12566801	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34224972	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4240931	0.90[ASN][1000 genomes]
rs4846731	0.83[ASN][1000 genomes]
rs6604682	0.82[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	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12562188	USH2A	cis	parietal	SCAN
rs12562188	MOSC1	cis	cerebellum	SCAN
rs12562188	C1orf115	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:222032800-222041600	Weak transcription	NHEK	skin
3	chr1:222032800-222041800	Weak transcription	Osteobl	bone
4	chr1:222033200-222041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:222038000-222040800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:222038000-222041800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:222038400-222041000	Enhancers	HMEC	breast
8	chr1:222039000-222041600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:222039600-222041600	Weak transcription	NHLF	lung
10	chr1:222039600-222041800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:222039800-222041600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:222039800-222041800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:222039800-222041800	Weak transcription	HSMM	muscle
14	chr1:222040000-222040600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:222040000-222041800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:222040200-222041400	Weak transcription	NHDF-Ad	bronchial
17	chr1:222040200-222041800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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