Variant report

Variant	rs2800018
Chromosome Location	chr6:64155904-64155905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTP4A1-6	chr6:64155652-64156647	NONHSAT113344

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10755410	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10806206	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12196062	0.81[ASN][1000 genomes]
rs1723535	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1741801	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1779747	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779748	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1969717	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096346	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186011	0.81[ASN][1000 genomes]
rs2622286	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622307	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753062	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2753066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800017	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800023	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800027	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800028	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4358600	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710255	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710430	0.82[ASN][1000 genomes]
rs6929702	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939983	0.81[ASN][1000 genomes]
rs7742595	0.84[ASN][1000 genomes]
rs7745873	0.82[ASN][1000 genomes]
rs7763834	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294215	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344129	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344137	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344168	0.81[ASN][1000 genomes]
rs9350913	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9352960	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9359467	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361762	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361767	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361779	0.84[ASN][1000 genomes]
rs9449291	0.81[ASN][1000 genomes]
rs9449297	0.82[ASN][1000 genomes]
rs9449312	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2800018	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
2	chr6:64152200-64157200	Weak transcription	Liver	Liver
3	chr6:64153600-64157000	Weak transcription	A549	lung
4	chr6:64155000-64156400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:64155000-64158000	Weak transcription	HepG2	liver
6	chr6:64155800-64156400	Enhancers	Stomach Smooth Muscle	stomach
7	chr6:64155800-64157000	Enhancers	Ovary	ovary
8	chr6:64155800-64158400	Enhancers	Skeletal Muscle Male	skeletal muscle

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