Variant report

Variant	rs2642541
Chromosome Location	chr12:58703475-58703476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1148533	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1174389	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1174594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1174600	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1185862	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1729796	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1729803	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2642539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2642541	LRP1	cis	parietal	SCAN
rs2642541	SMUG1	cis	cerebellum	SCAN
rs2642541	DTX3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58703000-58704000	Enhancers	NHLF	lung
2	chr12:58703000-58705600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr12:58703000-58705800	Enhancers	HMEC	breast
4	chr12:58703200-58703800	ZNF genes & repeats	A549	lung
5	chr12:58703200-58704400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:58703200-58704600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:58703200-58704800	Enhancers	Hela-S3	cervix
8	chr12:58703200-58704800	Enhancers	HUVEC	blood vessel
9	chr12:58703200-58705400	Enhancers	HSMM	muscle
10	chr12:58703200-58705600	Enhancers	NHEK	skin
11	chr12:58703400-58704000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:58703400-58705800	Enhancers	NHDF-Ad	bronchial

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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

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