Variant report

Variant	rs730760
Chromosome Location	chr12:41682754-41682755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10785188	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879915	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1367605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431122	0.91[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1431127	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830191	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1918239	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1946568	0.88[JPT][hapmap]
rs2049591	0.92[GIH][hapmap];0.84[TSI][hapmap]
rs2405905	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405907	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768000	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134405	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295866	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971349	0.80[EUR][1000 genomes]
rs7971896	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv469364	chr12:41631105-41710912	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv558699	chr12:41631105-41710912	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv558700	chr12:41665279-41710912	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs730760	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41671200-41684600	Weak transcription	Ovary	ovary
2	chr12:41680400-41683600	Enhancers	Fetal Kidney	kidney
3	chr12:41680600-41688000	Weak transcription	Aorta	Aorta
4	chr12:41681400-41682800	Enhancers	Brain Germinal Matrix	brain
5	chr12:41681800-41685800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:41682000-41683200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:41682000-41683400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:41682200-41687200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:41682400-41683400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:41682600-41683200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:41682600-41683800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:41682600-41685600	Weak transcription	Fetal Intestine Large	intestine

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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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