Variant report

Variant	rs62110427
Chromosome Location	chr19:21610180-21610181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-1	chr19:21608886-21610284	ENSG00000196686

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10414834	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424079	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11666213	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666447	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666525	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666540	0.81[EUR][1000 genomes]
rs11667361	0.81[EUR][1000 genomes]
rs11669033	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669790	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11670815	0.81[EUR][1000 genomes]
rs11670868	0.85[AMR][1000 genomes]
rs11672341	0.80[EUR][1000 genomes]
rs11672583	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13346641	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17680605	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967182	0.88[ASN][1000 genomes]
rs2061916	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2358993	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2359144	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2359145	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562405	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2562413	0.88[ASN][1000 genomes]
rs2562416	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2650776	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650844	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2650848	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3853837	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853838	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321312	0.81[EUR][1000 genomes]
rs4359573	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4544364	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4638726	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55756795	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55875743	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58412280	0.85[AMR][1000 genomes]
rs62107479	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62107531	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62107532	0.80[EUR][1000 genomes]
rs62107534	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62107536	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62107539	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62107540	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62107541	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109225	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109226	0.85[AMR][1000 genomes]
rs62109227	0.85[AMR][1000 genomes]
rs62109228	0.85[AMR][1000 genomes]
rs62109229	0.81[EUR][1000 genomes]
rs62110367	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62110377	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62110416	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110420	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110424	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110426	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110428	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110429	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7258099	0.80[EUR][1000 genomes]
rs7258473	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73537884	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs62110427	ZNF708	cis	Muscle Skeletal	GTEx
rs62110427	ZNF708	cis	Thyroid	GTEx
rs62110427	RP11-678G14.2	cis	Thyroid	GTEx
rs62110427	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs62110427	ZNF708	cis	lung	GTEx
rs62110427	RP11-678G14.2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
3	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:21604400-21610400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:21605600-21610800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:21605600-21610800	Weak transcription	Ovary	ovary
8	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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