Variant report

Variant	rs11177604
Chromosome Location	chr12:41045385-41045386
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10161139	0.83[ASN][1000 genomes]
rs10748131	0.85[ASN][1000 genomes]
rs10784786	0.85[ASN][1000 genomes]
rs10879003	0.85[ASN][1000 genomes]
rs11177713	0.85[ASN][1000 genomes]
rs11177722	0.86[ASN][1000 genomes]
rs11177948	0.83[ASN][1000 genomes]
rs1348511	0.86[ASN][1000 genomes]
rs1348513	0.85[ASN][1000 genomes]
rs1373428	0.85[ASN][1000 genomes]
rs1373429	0.85[ASN][1000 genomes]
rs1444209	0.85[ASN][1000 genomes]
rs1816857	0.86[ASN][1000 genomes]
rs1838342	0.87[ASN][1000 genomes]
rs2083957	0.86[ASN][1000 genomes]
rs4445719	0.86[ASN][1000 genomes]
rs4548695	0.86[ASN][1000 genomes]
rs7309561	0.85[ASN][1000 genomes]
rs7973726	0.85[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	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv832378	chr12:40943111-41132305	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11177604	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41044200-41045400	Enhancers	H1 Cell Line	embryonic stem cell
2	chr12:41044600-41045600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr12:41045200-41045600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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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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