Variant report

Variant	rs2642539
Chromosome Location	chr12:58711151-58711152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1148533	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1174389	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1174594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1174600	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1185862	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1729796	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1729803	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2642541	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv899124	chr12:58391839-58883507	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv730	chr12:58698792-58759096	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1035772	chr12:58708608-58732055	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2642539	LRP1	cis	parietal	SCAN
rs2642539	SMUG1	cis	cerebellum	SCAN
rs2642539	DTX3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58709200-58721200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:58710000-58711400	Enhancers	Fetal Intestine Large	intestine
3	chr12:58710800-58711200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:58711000-58711600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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