Variant report

Variant	rs10401980
Chromosome Location	chr19:40655002-40655003
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10406471	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1327185	0.89[ASN][1000 genomes]
rs1327187	0.86[ASN][1000 genomes]
rs1327188	0.90[ASN][1000 genomes]
rs1327189	0.91[ASN][1000 genomes]
rs1327190	0.91[ASN][1000 genomes]
rs1327191	0.91[ASN][1000 genomes]
rs1327192	0.91[ASN][1000 genomes]
rs1327193	0.91[ASN][1000 genomes]
rs13344062	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16974093	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17797100	0.92[ASN][1000 genomes]
rs1854098	0.89[ASN][1000 genomes]
rs186815	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1998931	0.91[ASN][1000 genomes]
rs24135	0.89[ASN][1000 genomes]
rs24136	0.89[ASN][1000 genomes]
rs24137	0.89[ASN][1000 genomes]
rs2569639	0.91[ASN][1000 genomes]
rs2569640	0.91[ASN][1000 genomes]
rs2569641	0.91[ASN][1000 genomes]
rs2569642	0.91[ASN][1000 genomes]
rs2569643	0.89[ASN][1000 genomes]
rs2569644	0.89[ASN][1000 genomes]
rs2569645	0.89[ASN][1000 genomes]
rs2569648	0.89[ASN][1000 genomes]
rs2569649	0.89[ASN][1000 genomes]
rs2569650	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2569651	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2767592	0.89[ASN][1000 genomes]
rs2767593	0.89[ASN][1000 genomes]
rs2767594	0.88[ASN][1000 genomes]
rs2767595	0.89[ASN][1000 genomes]
rs2767596	0.89[ASN][1000 genomes]
rs2767597	0.89[ASN][1000 genomes]
rs2767598	0.89[ASN][1000 genomes]
rs2767601	0.90[ASN][1000 genomes]
rs2767603	0.91[ASN][1000 genomes]
rs2767604	0.89[ASN][1000 genomes]
rs2767605	0.89[ASN][1000 genomes]
rs2767606	0.89[ASN][1000 genomes]
rs2767607	0.89[ASN][1000 genomes]
rs2767608	0.89[ASN][1000 genomes]
rs2767609	0.89[ASN][1000 genomes]
rs2819955	0.89[ASN][1000 genomes]
rs2819958	0.91[ASN][1000 genomes]
rs28629274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28890790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915972	0.87[ASN][1000 genomes]
rs2970102	0.89[ASN][1000 genomes]
rs337784	0.89[ASN][1000 genomes]
rs337785	0.89[ASN][1000 genomes]
rs337786	0.89[ASN][1000 genomes]
rs337787	0.89[ASN][1000 genomes]
rs337788	0.89[ASN][1000 genomes]
rs337789	0.89[ASN][1000 genomes]
rs337790	0.89[ASN][1000 genomes]
rs337791	0.88[ASN][1000 genomes]
rs337792	0.89[ASN][1000 genomes]
rs337793	0.89[ASN][1000 genomes]
rs337794	0.89[ASN][1000 genomes]
rs337799	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs337800	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs337801	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58003479	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58899236	0.89[ASN][1000 genomes]
rs73549877	0.88[ASN][1000 genomes]
rs73551642	0.91[ASN][1000 genomes]
rs73551661	0.92[ASN][1000 genomes]
rs73551662	0.92[ASN][1000 genomes]
rs73551663	0.92[ASN][1000 genomes]
rs73551668	0.92[ASN][1000 genomes]
rs73551674	0.92[ASN][1000 genomes]
rs73551675	0.92[ASN][1000 genomes]
rs73551681	0.92[ASN][1000 genomes]
rs73551683	0.91[ASN][1000 genomes]
rs73551685	0.92[ASN][1000 genomes]
rs73551687	0.92[ASN][1000 genomes]
rs73551688	0.92[ASN][1000 genomes]
rs73551689	0.92[ASN][1000 genomes]
rs73551691	0.92[ASN][1000 genomes]
rs73551695	0.93[ASN][1000 genomes]
rs73553603	0.84[ASN][1000 genomes]
rs8103294	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv3336591	chr19:40647161-40670363	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10401980	ZNF780A	cis	Thyroid	GTEx
rs10401980	ZNF780A	cis	lung	GTEx
rs10401980	AC005614.5	cis	lung	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40654200-40673400	Weak transcription	Right Atrium	heart
2	chr19:40654400-40655400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:40654400-40658200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:40654400-40658600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:40654400-40661000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:40654600-40655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:40654600-40655600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:40654600-40655600	Weak transcription	Adipose Nuclei	Adipose
9	chr19:40654800-40656200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr19:40654800-40658600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:40655000-40656000	Weak transcription	Primary monocytes fromperipheralblood	blood

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