Variant report

Variant	rs13228575
Chromosome Location	chr7:64296126-64296127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF117-4	chr7:64295658-64297260	NONHSAT121041

Extended variants
information (count: 70 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10085758	0.81[ASN][1000 genomes]
rs10155953	0.84[ASN][1000 genomes]
rs10225171	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10231007	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10244479	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10251806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267321	0.87[AMR][1000 genomes]
rs10267350	0.87[AMR][1000 genomes]
rs10279535	0.84[AMR][1000 genomes]
rs10949946	0.86[EUR][1000 genomes]
rs10949947	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760727	0.80[EUR][1000 genomes]
rs11974982	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12154509	0.89[AMR][1000 genomes]
rs13226426	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13230564	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464927	0.82[EUR][1000 genomes]
rs1464928	0.82[EUR][1000 genomes]
rs1815166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1815167	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880656	0.82[EUR][1000 genomes]
rs2015939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863927	0.81[ASN][1000 genomes]
rs28878851	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3763506	0.82[EUR][1000 genomes]
rs4273745	0.86[AMR][1000 genomes]
rs4386865	0.88[AMR][1000 genomes]
rs4518551	0.82[EUR][1000 genomes]
rs4613868	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4717217	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718125	0.82[EUR][1000 genomes]
rs4718131	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718142	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55683815	0.80[EUR][1000 genomes]
rs56004721	0.82[EUR][1000 genomes]
rs56075681	0.82[EUR][1000 genomes]
rs57570718	0.83[EUR][1000 genomes]
rs60113999	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460195	0.82[EUR][1000 genomes]
rs6961445	0.80[EUR][1000 genomes]
rs73130313	0.82[AMR][1000 genomes]
rs73130314	0.82[AMR][1000 genomes]
rs73142749	0.80[EUR][1000 genomes]
rs7781361	0.83[ASN][1000 genomes]
rs7783765	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785735	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7787287	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7790203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792444	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7793057	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7802289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809177	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7810067	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][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	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
7	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv15396	chr7:64295355-64301341	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs13228575	SEPHS1P1	cis	Esophagus Mucosa	GTEx
rs13228575	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs13228575	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs13228575	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs13228575	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs13228575	RP11-797H7.3	cis	Thyroid	GTEx
rs13228575	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs13228575	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs13228575	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs13228575	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs13228575	SEPHS1P1	cis	Muscle Skeletal	GTEx
rs13228575	RP11-797H7.3	cis	Stomach	GTEx
rs13228575	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13228575	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs13228575	RP11-797H7.3	cis	lung	GTEx
rs13228575	RP11-460N20.5	cis	Thyroid	GTEx
rs13228575	SEPHS1P1	cis	Adipose Subcutaneous	GTEx
rs13228575	RP11-797H7.3	cis	Artery Tibial	GTEx
rs13228575	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs13228575	RP11-797H7.3	cis	Artery Aorta	GTEx
rs13228575	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs13228575	SEPHS1P1	cis	Thyroid	GTEx
rs13228575	RP11-797H7.3	cis	Whole Blood	GTEx
rs13228575	SEPHS1P1	cis	Artery Tibial	GTEx
rs13228575	SEPHS1P1	cis	Nerve Tibial	GTEx
rs13228575	RP11-797H7.5	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64273400-64301400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:64284800-64299800	Weak transcription	Pancreas	Pancrea
3	chr7:64285400-64296400	Weak transcription	Left Ventricle	heart
4	chr7:64293000-64296600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:64293000-64301000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:64296000-64296400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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