Variant report

Variant	rs9942389
Chromosome Location	chr5:167362446-167362447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10065576	0.89[YRI][hapmap]
rs10075943	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10475524	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10475862	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11134481	0.93[EUR][1000 genomes]
rs35278978	0.92[AFR][1000 genomes]
rs56738437	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62384403	0.90[EUR][1000 genomes]
rs62384408	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62384409	0.87[EUR][1000 genomes]
rs6882229	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6886222	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7735238	0.82[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830546	chr5:167303135-167456271	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9942389	LOC93622	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167352000-167364400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:167361200-167364600	Active TSS	Right Atrium	heart
3	chr5:167361600-167362800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:167361600-167366800	Weak transcription	NH-A	brain
5	chr5:167361600-167371200	Weak transcription	NHEK	skin
6	chr5:167361800-167365000	Active TSS	Left Ventricle	heart
7	chr5:167361800-167366800	Active TSS	Right Ventricle	heart
8	chr5:167362000-167362600	Enhancers	Fetal Heart	heart
9	chr5:167362200-167363000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:167362200-167364600	Weak transcription	Aorta	Aorta
11	chr5:167362200-167370000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:167362400-167362600	Active TSS	HSMMtube	muscle
13	chr5:167362400-167362800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:167362400-167363800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:167362400-167363800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:167362400-167364400	Weak transcription	HSMM	muscle
17	chr5:167362400-167364800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:167362400-167367200	Weak transcription	HMEC	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