Variant report

Variant	rs2609942
Chromosome Location	chr2:30924850-30924851
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12052219	0.82[CHB][hapmap]
rs12618680	0.81[AMR][1000 genomes]
rs12986790	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13021296	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17041364	0.84[EUR][1000 genomes]
rs2593437	0.81[CEU][hapmap]
rs2681686	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681687	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2946928	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346433	0.86[ASN][1000 genomes]
rs4952177	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7601114	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv32718	chr2:30918546-30926192	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2609942	LCLAT1	cis	parietal	SCAN
rs2609942	KHK	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30902400-30954000	Weak transcription	Gastric	stomach
2	chr2:30918600-30925000	Weak transcription	Fetal Heart	heart
3	chr2:30923600-30926200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:30924800-30925600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:30924800-30925600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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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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