Variant report

Variant	rs9350913
Chromosome Location	chr6:64146936-64146937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGSN-3	chr6:64146297-64147330	l_3198_chr6:64146296-64150277_placenta

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10755410	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10806206	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1723535	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1741801	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1779747	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779748	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1969717	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076874	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096346	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2622286	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2622307	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2753062	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2753066	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800017	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800018	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800023	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800027	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800028	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4358600	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4710255	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4710431	0.81[ASN][1000 genomes]
rs6929702	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7742595	0.81[ASN][1000 genomes]
rs7763834	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9294215	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9344129	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9344137	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9352960	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9359467	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9361762	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361767	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9361779	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	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
rs9350913	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64149400	Weak transcription	A549	lung
2	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
3	chr6:64146800-64149600	Weak transcription	HepG2	liver

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