Variant report

Variant	rs1245424
Chromosome Location	chr12:62522039-62522040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1146077	0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs1146078	0.88[ASN][1000 genomes]
rs1146080	0.87[ASN][1000 genomes]
rs1146081	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs1146082	0.96[ASN][1000 genomes]
rs1146083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs348638	0.92[CHB][hapmap]
rs348652	0.92[CHB][hapmap]
rs348654	0.92[CHB][hapmap]

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	nsv832435	chr12:62407000-62601835	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv559154	chr12:62509757-62522787	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1245424	GLI1	cis	parietal	SCAN
rs1245424	PRR5	trans	cerebellum	SCAN
rs1245424	C6orf186	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62519800-62525600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:62521400-62522400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:62521400-62522600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:62521400-62522600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:62521400-62522600	Enhancers	HMEC	breast
6	chr12:62521600-62522200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:62521600-62522200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:62521600-62522600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:62521800-62522400	Enhancers	NHEK	skin
10	chr12:62522000-62523000	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:62522000-62523000	Bivalent Enhancer	HUVEC	blood vessel

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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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