Variant report

Variant	rs12479580
Chromosome Location	chr20:52594079-52594080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs169639	0.81[JPT][hapmap]
rs208389	0.85[JPT][hapmap]
rs2276498	0.80[CEU][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs2276499	0.80[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs2276507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6123336	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs6123338	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs6127054	0.80[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs6127055	0.89[JPT][hapmap]

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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12479580	CSTF1	cis	cerebellum	SCAN
rs12479580	C20orf106	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52580800-52600000	Weak transcription	Stomach Mucosa	stomach
3	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52591200-52597000	Strong transcription	HSMMtube	muscle
5	chr20:52592000-52599600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52592200-52595200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:52592800-52599600	Weak transcription	Brain Hippocampus Middle	brain
8	chr20:52593000-52600800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:52593200-52601000	Weak transcription	Brain Substantia Nigra	brain

Quick Search:

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

what's new

Quick links