Variant report

Variant	rs12506696
Chromosome Location	chr4:130298617-130298618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12506624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510624	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1433378	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4440237	0.86[ASN][1000 genomes]
rs4540061	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55792344	0.94[EUR][1000 genomes]
rs55875663	0.82[EUR][1000 genomes]
rs56108227	0.82[EUR][1000 genomes]
rs56265309	0.84[EUR][1000 genomes]
rs56361313	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56690775	0.82[EUR][1000 genomes]
rs56982957	0.93[EUR][1000 genomes]
rs61070104	0.82[EUR][1000 genomes]
rs61455970	0.98[EUR][1000 genomes]
rs61554187	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62309611	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62309616	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62317276	1.00[AFR][1000 genomes];0.98[EUR][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	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv830058	chr4:130136025-130315471	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12506696	LCA5	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130297600-130299400	Enhancers	HUVEC	blood vessel
2	chr4:130298000-130298800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:130298000-130300000	Enhancers	Fetal Heart	heart
4	chr4:130298200-130298800	Enhancers	Dnd41	blood
5	chr4:130298200-130299000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:130298400-130298800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:130298400-130298800	Flanking Active TSS	HMEC	breast
8	chr4:130298600-130298800	Flanking Active TSS	NHEK	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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