Variant report

Variant	rs2299542
Chromosome Location	chr7:126785856-126785857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10954143	0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1361955	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1858784	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040502	0.87[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs2106183	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2237785	0.83[JPT][hapmap]
rs2283094	0.89[JPT][hapmap]
rs2299533	0.86[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2299540	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2402855	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950264	0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs7808643	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs978874	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889189	chr7:126699088-126963028	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2761367	chr7:126717157-126865324	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1027369	chr7:126772111-126798871	Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2299542	CCDC136	cis	parietal	SCAN
rs2299542	IQUB	cis	cerebellum	SCAN
rs2299542	IQUB	cis	parietal	SCAN
rs2299542	TMEM209	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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