Variant report

Variant	rs13423458
Chromosome Location	chr2:36958829-36958830
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1015696	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10189264	0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs10189296	0.83[CHB][hapmap]
rs10201689	0.94[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13397655	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13398046	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13423449	0.83[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17019636	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17019638	1.00[ASW][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17019641	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4670166	0.87[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs66497336	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66773952	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67756954	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7572548	0.94[CHB][hapmap];0.94[JPT][hapmap]

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	nsv1007757	chr2:36838387-37011384	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv535643	chr2:36838387-37011384	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2762493	chr2:36958342-36965718	Weak transcription Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13423458	OMP	trans	parietal	SCAN
rs13423458	STRN	cis	parietal	SCAN
rs13423458	MYADML	cis	parietal	SCAN
rs13423458	FAM98A	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36941000-36960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:36942600-36968800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:36957000-36959200	Weak transcription	NHDF-Ad	bronchial
4	chr2:36957800-36959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:36958000-36962000	Enhancers	Hela-S3	cervix
6	chr2:36958000-36968200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:36958000-36970800	Weak transcription	Ovary	ovary
8	chr2:36958200-36960600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:36958200-36963600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:36958800-36959600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:36958800-36960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:36958800-36960200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:36958800-36961000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:36958800-36961000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:36958800-36961600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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