Variant report

Variant	rs7469568
Chromosome Location	chr9:22767767-22767768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRTA1-1	chr9:22767106-22768486	NONHSAT130449

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10811771	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10811772	0.88[AMR][1000 genomes]
rs10965442	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10965450	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10965451	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12335498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12339358	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12341759	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12345463	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12346016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12348692	0.80[AMR][1000 genomes]
rs12349560	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13285009	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1349150	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1349151	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1375292	0.94[ASN][1000 genomes]
rs2067015	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2383242	0.88[JPT][hapmap]
rs35078908	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35881086	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62574663	0.80[EUR][1000 genomes]
rs6475677	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66678376	0.89[AMR][1000 genomes]
rs7033189	0.80[ASN][1000 genomes]
rs7863302	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9695226	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9696424	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1016037	chr9:22703983-22929532	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv892765	chr9:22705094-22847961	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2761290	chr9:22724129-22784718	Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1019512	chr9:22733238-22771006	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv613788	chr9:22739631-22784110	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1020027	chr9:22740232-22778492	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1026544	chr9:22740232-22789354	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1030847	chr9:22740232-22795971	Enhancers Weak transcription Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv540091	chr9:22746313-22778766	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7469568	RP11-370B11.3	cis	Esophagus Mucosa	GTEx
rs7469568	RP11-399D6.2	cis	Thyroid	GTEx
rs7469568	RP11-370B11.3	cis	Adipose Subcutaneous	GTEx
rs7469568	RP11-370B11.3	cis	Esophagus Muscularis	GTEx
rs7469568	RP11-399D6.2	cis	Esophagus Muscularis	GTEx
rs7469568	RP11-399D6.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22725800-22801600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:22738800-22778800	Weak transcription	Liver	Liver
3	chr9:22763800-22803600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:22767600-22770200	Weak transcription	Adipose Nuclei	Adipose

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