Variant report

Variant	rs10879844
Chromosome Location	chr12:41592149-41592150
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10506183	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10506184	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10879842	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10879924	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11180331	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180534	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11611769	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11612056	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11614877	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12369121	0.89[EUR][1000 genomes]
rs17129192	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7311069	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10879844	CNTN1	cis	temporal cortex	BrainEAC

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41585400-41599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:41589800-41592400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:41590000-41592800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:41590600-41599000	Weak transcription	Rectal Smooth Muscle	rectum

Quick Search:

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

what's new

Quick links