Variant report

Variant	rs7561688
Chromosome Location	chr2:58233464-58233465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1016771	0.95[MEX][hapmap]
rs10172295	1.00[ASW][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13011711	0.91[MEX][hapmap]
rs13014613	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13033536	0.83[AMR][1000 genomes]
rs1518401	1.00[YRI][hapmap]
rs17049305	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2030237	1.00[ASW][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs2717039	0.82[MEX][hapmap]
rs4672226	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4672228	0.86[AMR][1000 genomes]
rs4672229	1.00[YRI][hapmap]
rs6717480	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7568266	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848291	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv458041	chr2:58196110-58237724	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv582096	chr2:58196110-58237724	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7561688	SMEK2	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