Variant report

Variant	rs208255
Chromosome Location	chr20:41413840-41413841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs114094	0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs17749217	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1885834	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1973949	0.81[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs208254	0.81[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs208256	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs55651075	0.81[ASN][1000 genomes]
rs59111183	0.89[ASN][1000 genomes]
rs6030468	0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs6103038	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6103040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6103041	0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs73098049	0.81[ASN][1000 genomes]
rs8119733	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][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	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs208255	DNTTIP1	cis	cerebellum	SCAN
rs208255	SDC4	cis	cerebellum	SCAN
rs208255	TOMM34	cis	parietal	SCAN
rs208255	CTSA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41407400-41420800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:41413800-41414600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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