Variant report

Variant	rs28498118
Chromosome Location	chr19:21647585-21647586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11085450	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11666680	0.83[ASN][1000 genomes]
rs11667259	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668682	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11668691	0.81[ASN][1000 genomes]
rs11669043	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11669130	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11671265	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12609768	0.81[AMR][1000 genomes]
rs12609823	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610154	0.83[ASN][1000 genomes]
rs2133819	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2133822	0.83[ASN][1000 genomes]
rs2650774	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28898308	0.82[ASN][1000 genomes]
rs34152818	0.82[ASN][1000 genomes]
rs34497957	0.81[ASN][1000 genomes]
rs35994743	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3973190	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4306654	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4462731	0.82[ASN][1000 genomes]
rs4621113	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56346453	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6511245	0.81[ASN][1000 genomes]
rs6511246	0.81[ASN][1000 genomes]
rs6511255	0.81[ASN][1000 genomes]
rs7245729	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246883	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247060	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248989	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7250838	0.81[ASN][1000 genomes]
rs7251620	0.84[ASN][1000 genomes]
rs7252254	0.83[ASN][1000 genomes]
rs7253886	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7257186	0.82[ASN][1000 genomes]
rs7259311	0.81[ASN][1000 genomes]
rs73017722	0.82[ASN][1000 genomes]
rs8101089	0.83[ASN][1000 genomes]
rs8101900	0.82[ASN][1000 genomes]
rs8106840	0.82[ASN][1000 genomes]
rs8111549	0.88[ASN][1000 genomes]
rs924487	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951162	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9973240	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs28498118	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs28498118	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28498118	RP11-678G14.3	cis	Whole Blood	GTEx
rs28498118	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28498118	CTD-2561J22.5	cis	Thyroid	GTEx
rs28498118	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs28498118	RP11-678G14.2	cis	lung	GTEx
rs28498118	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs28498118	RP11-678G14.2	cis	Artery Tibial	GTEx
rs28498118	RP11-678G14.2	cis	Whole Blood	GTEx
rs28498118	ZNF429	cis	Whole Blood	GTEx
rs28498118	ZNF429	cis	Muscle Skeletal	GTEx
rs28498118	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs28498118	RP11-678G14.3	cis	lung	GTEx
rs28498118	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs28498118	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs28498118	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs28498118	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs28498118	RP11-678G14.2	cis	Thyroid	GTEx
rs28498118	ZNF100	cis	Muscle Skeletal	GTEx
rs28498118	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs28498118	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs28498118	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs28498118	LINC00664	cis	Adipose Subcutaneous	GTEx
rs28498118	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs28498118	CTD-2561J22.5	cis	lung	GTEx
rs28498118	CTD-2561J22.5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21647000-21649200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:21647000-21657200	Weak transcription	Right Atrium	heart
3	chr19:21647200-21647800	Enhancers	Dnd41	blood
4	chr19:21647200-21651600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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