Variant report

Variant	rs2622286
Chromosome Location	chr6:64150067-64150068
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:64150043-64150327	A549	lung:	n/a	n/a
2	POLR2A	chr6:64150039-64150341	HCT-116	colon:	n/a	n/a
3	POU2F2	chr6:64149996-64150345	GM12891	blood:	n/a	n/a
4	MAX	chr6:64149902-64150712	A549	lung:	n/a	n/a
5	POLR2A	chr6:64150015-64150369	A549	lung:	n/a	n/a
6	REST	chr6:64150025-64150974	A549	lung:	n/a	n/a
7	POLR2A	chr6:64150044-64150325	A549	lung:	n/a	n/a
8	MAX	chr6:64149946-64150207	A549	lung:	n/a	n/a
9	TAF1	chr6:64149908-64150650	A549	lung:	n/a	n/a
10	POLR2A	chr6:64150066-64150308	A549	lung:	n/a	n/a
11	POLR2A	chr6:64150039-64150314	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000218048	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10755410	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10806206	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12196062	0.81[ASN][1000 genomes]
rs1723535	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1741801	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1779747	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779748	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1969717	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076874	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186011	0.81[ASN][1000 genomes]
rs2622307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753062	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2753066	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800018	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800027	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800028	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4358600	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4445042	0.81[EUR][1000 genomes]
rs4710254	0.81[EUR][1000 genomes]
rs4710255	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710430	0.82[ASN][1000 genomes]
rs6919709	0.81[EUR][1000 genomes]
rs6929702	0.89[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	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294196	0.81[EUR][1000 genomes]
rs9294197	0.81[EUR][1000 genomes]
rs9294198	0.81[EUR][1000 genomes]
rs9294206	0.81[EUR][1000 genomes]
rs9294215	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9341841	0.81[EUR][1000 genomes]
rs9344090	0.81[EUR][1000 genomes]
rs9344129	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344168	0.81[ASN][1000 genomes]
rs9350913	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9352960	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9359467	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361762	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361767	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361779	0.84[ASN][1000 genomes]
rs9449233	0.81[EUR][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
rs2622286	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
2	chr6:64149400-64152400	Active TSS	A549	lung
3	chr6:64149600-64152400	Enhancers	HepG2	liver
4	chr6:64149800-64150400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:64150000-64150400	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:64150000-64150400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:64150000-64150600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:64150000-64150600	Enhancers	Placenta	Placenta
9	chr6:64150000-64150800	Enhancers	Stomach Mucosa	stomach

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