Variant report

Variant	rs9749140
Chromosome Location	chr19:56939052-56939053
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10408270	0.87[EUR][1000 genomes]
rs10408604	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10413169	0.85[ASN][1000 genomes]
rs10415307	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10416345	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419332	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10421407	0.83[ASN][1000 genomes]
rs10432288	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11084446	0.83[EUR][1000 genomes]
rs11084449	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084450	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667815	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12460342	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608966	0.83[EUR][1000 genomes]
rs12610115	0.87[EUR][1000 genomes]
rs12973407	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981146	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12981443	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1988918	0.82[AFR][1000 genomes]
rs2288860	0.82[EUR][1000 genomes]
rs28373215	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2904016	0.82[EUR][1000 genomes]
rs2904017	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35027158	0.85[ASN][1000 genomes]
rs35869148	0.85[ASN][1000 genomes]
rs35914474	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745826	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3760849	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3810340	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4281830	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4801163	0.83[ASN][1000 genomes]
rs4801319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56301546	0.85[EUR][1000 genomes]
rs59858465	0.85[EUR][1000 genomes]
rs62121590	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62121593	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248278	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250817	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252607	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258010	0.82[EUR][1000 genomes]
rs728232	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104319	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104585	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8112531	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112935	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917650	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917651	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917652	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304776	0.82[ASN][1000 genomes]
rs9789281	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	esv1792699	chr19:56931672-56950997	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9749140	ZNF582-AS1	cis	lung	GTEx
rs9749140	ZNF582-AS1	cis	Artery Tibial	GTEx
rs9749140	ZNF582-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56916400-56956000	ZNF genes & repeats	Liver	Liver
2	chr19:56916600-56956000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:56917000-56940000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:56917400-56944800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:56917600-56939400	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr19:56918200-56940000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:56918200-56940600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
8	chr19:56918200-56943400	ZNF genes & repeats	Brain Anterior Caudate	brain
9	chr19:56918400-56942800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:56918400-56945400	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:56928200-56939800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:56931200-56944400	ZNF genes & repeats	Brain Substantia Nigra	brain
13	chr19:56931400-56939800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
14	chr19:56931400-56940000	ZNF genes & repeats	Colon Smooth Muscle	Colon
15	chr19:56931400-56940400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
16	chr19:56931400-56940600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
17	chr19:56938200-56940000	ZNF genes & repeats	Fetal Lung	lung
18	chr19:56938400-56940000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
19	chr19:56938400-56940600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain

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