Variant report

Variant	rs2049591
Chromosome Location	chr12:41653366-41653367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10785188	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10879915	0.86[EUR][1000 genomes]
rs11180604	0.84[AFR][1000 genomes]
rs1367605	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs1431122	0.82[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1431127	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1830191	0.80[EUR][1000 genomes]
rs1918239	0.82[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2405905	0.80[EUR][1000 genomes]
rs4768000	0.80[EUR][1000 genomes]
rs730760	0.92[GIH][hapmap];0.84[TSI][hapmap]
rs7965249	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs7971349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2049591	CNTN1	cis	cerebellum	SCAN
rs2049591	ABCD2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41644800-41657200	Weak transcription	Ovary	ovary
2	chr12:41651200-41661000	Weak transcription	Colon Smooth Muscle	Colon

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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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