Variant report

Variant	rs2090602
Chromosome Location	chr11:45852646-45852647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10838521	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11038673	0.89[YRI][hapmap]
rs11038677	0.87[ASN][1000 genomes]
rs1139266	0.94[JPT][hapmap]
rs2002244	0.92[ASN][1000 genomes]
rs2292912	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3824872	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4756037	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6798	0.82[GIH][hapmap]
rs7105609	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7115967	0.82[CHD][hapmap]
rs7951225	0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2090602	F2	cis	cerebellum	SCAN
rs2090602	CRY2	cis	multi-tissue	Pritchard
rs2090602	NTRK3	trans	cerebellum	SCAN
rs2090602	AGBL2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45845800-45869000	Weak transcription	Right Atrium	heart
2	chr11:45846000-45855800	Weak transcription	Ovary	ovary
3	chr11:45848400-45855800	Weak transcription	Left Ventricle	heart
4	chr11:45851000-45854000	Weak transcription	Placenta	Placenta
5	chr11:45851600-45853200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr11:45851800-45852800	Weak transcription	Psoas Muscle	Psoas
7	chr11:45851800-45853600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr11:45851800-45855800	Weak transcription	Adipose Nuclei	Adipose
9	chr11:45852400-45853600	Enhancers	Brain Angular Gyrus	brain

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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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