Variant report

Variant	rs744638
Chromosome Location	chr2:31236407-31236408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1862969	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161831	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs744638	CAPN13	cis	parietal	SCAN
rs744638	ALK	cis	cerebellum	SCAN
rs744638	KRTCAP3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31232600-31251000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:31235200-31236600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:31235200-31236800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr2:31235200-31251000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:31235400-31251000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:31236400-31237200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:31236400-31249400	Weak transcription	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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