Variant report

Variant	rs1779748
Chromosome Location	chr6:64141709-64141710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10755410	0.81[EUR][1000 genomes]
rs10806206	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723535	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1741801	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1779747	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969717	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076874	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096346	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622286	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622307	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2753062	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2753066	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800017	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800018	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800023	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800027	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800028	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4445042	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710254	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710255	0.81[EUR][1000 genomes]
rs6919709	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929702	0.81[EUR][1000 genomes]
rs9294196	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294197	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294198	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294202	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294206	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294215	0.81[EUR][1000 genomes]
rs9341841	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344090	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344129	0.81[EUR][1000 genomes]
rs9344137	0.80[EUR][1000 genomes]
rs9350913	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9449233	0.88[EUR][1000 genomes];0.85[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	nsv538270	chr6:63682752-64147241	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1779748	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64133400-64144600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:64139800-64145200	Enhancers	HepG2	liver
3	chr6:64140200-64144800	Weak transcription	A549	lung
4	chr6:64141000-64142200	Active TSS	Fetal Intestine Large	intestine

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