Variant report

Variant	rs2562398
Chromosome Location	chr19:21722949-21722950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:21722139-21723126	K562	blood:	n/a	n/a

Variant related genes	Relation type
ZNF429	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10420016	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10854048	0.89[ASN][1000 genomes]
rs10854050	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10854051	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085462	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085463	0.84[ASN][1000 genomes]
rs11085465	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085468	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668606	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671579	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974758	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1879234	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2173727	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2359155	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2562408	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562417	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562428	0.83[AFR][1000 genomes]
rs2562456	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562466	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562468	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562471	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562487	0.83[AFR][1000 genomes]
rs2562507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650784	0.84[EUR][1000 genomes]
rs2650792	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2650793	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650804	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650805	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2650825	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681370	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2681377	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2681388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681389	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681391	0.81[EUR][1000 genomes]
rs2681392	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681395	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2946790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35008138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35099594	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55771551	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58001930	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62110202	0.82[EUR][1000 genomes]
rs6511250	0.86[EUR][1000 genomes]
rs6511253	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511254	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511256	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511258	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7252585	0.83[EUR][1000 genomes]
rs7259708	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304986	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9304987	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2562398	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562398	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2562398	ZNF708	cis	lung	GTEx
rs2562398	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562398	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562398	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562398	ZNF708	cis	Muscle Skeletal	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
2	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21714600-21723000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr19:21715200-21728600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:21719600-21729400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:21720000-21724200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr19:21720000-21724200	Weak transcription	HSMM	muscle
8	chr19:21720000-21724600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:21720000-21724800	Weak transcription	Thymus	Thymus
10	chr19:21720000-21727400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:21720200-21724400	Weak transcription	Stomach Mucosa	stomach
12	chr19:21720200-21724800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:21720200-21725000	Weak transcription	Right Ventricle	heart
14	chr19:21720400-21724400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:21720400-21724600	Weak transcription	Ovary	ovary
16	chr19:21720400-21724800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:21720400-21725000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:21720400-21740800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:21720600-21724400	Weak transcription	Fetal Lung	lung
20	chr19:21720600-21724600	Weak transcription	Brain Germinal Matrix	brain
21	chr19:21720800-21724200	Weak transcription	Brain Anterior Caudate	brain
22	chr19:21720800-21724400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:21720800-21725000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:21720800-21725600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:21720800-21729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:21721600-21728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:21721800-21724400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:21722600-21724400	Weak transcription	Fetal Intestine Small	intestine
29	chr19:21722600-21724400	Weak transcription	Placenta	Placenta
30	chr19:21722600-21725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:21722800-21724200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:21722800-21724200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:21722800-21727200	Weak transcription	Osteobl	bone
34	chr19:21722800-21727600	Weak transcription	Psoas Muscle	Psoas

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