Variant report

Variant	rs1744143
Chromosome Location	chr6:64220833-64220834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10943869	0.85[EUR][1000 genomes]
rs13200519	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13205487	0.83[EUR][1000 genomes]
rs13217662	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1744134	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1744153	0.90[ASN][1000 genomes]
rs1779739	0.87[EUR][1000 genomes]
rs1779777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025178	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489272	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622312	0.87[ASN][1000 genomes]
rs2758244	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3121608	0.81[EUR][1000 genomes]
rs6916092	0.84[EUR][1000 genomes]
rs71534831	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7753325	0.82[ASN][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	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv970333	chr6:64215926-64234330	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1744143	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64219000-64221600	Enhancers	Fetal Intestine Large	intestine
2	chr6:64219600-64221000	Enhancers	Colon Smooth Muscle	Colon
3	chr6:64219600-64221200	Enhancers	Duodenum Mucosa	Duodenum
4	chr6:64219600-64221200	Enhancers	Fetal Intestine Small	intestine
5	chr6:64219600-64221200	Enhancers	Stomach Mucosa	stomach
6	chr6:64220000-64221000	Enhancers	Pancreas	Pancrea
7	chr6:64220000-64221000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:64220000-64224200	Enhancers	HepG2	liver
9	chr6:64220200-64222600	Weak transcription	Fetal Lung	lung
10	chr6:64220200-64224000	Enhancers	A549	lung
11	chr6:64220200-64229200	Weak transcription	NHEK	skin
12	chr6:64220400-64224000	Weak transcription	Hela-S3	cervix
13	chr6:64220400-64224800	Enhancers	Liver	Liver
14	chr6:64220600-64227600	Weak transcription	GM12878-XiMat	blood
15	chr6:64220800-64221000	Enhancers	Breast Myoepithelial Primary Cells	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