Variant report

Variant	rs2562456
Chromosome Location	chr19:21666210-21666211
allele	A/G
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	ZNF263	chr19:21665697-21666246	K562	blood:	n/a	n/a
2	CTCF	chr19:21665466-21666273	SK-N-SH	brain:	n/a	chr19:21665789-21665802 chr19:21665753-21665771 chr19:21665755-21665768 chr19:21665874-21665887 chr19:21665754-21665770 chr19:21665755-21665768

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF429-1	chr19:21666176-21666333	ENSG00000248094
2	lnc-ZNF429-1	chr19:21666176-21666333	NONHSAT063711
3	lnc-ZNF429-1	chr19:21666176-21666333	ENSG00000268658.1

Variant related genes	Relation type
LINC00664	TF binding region

Extended variants
information (count: 110 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10420016	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10424079	0.83[CEU][hapmap]
rs1055753	0.81[JPT][hapmap]
rs11085441	0.82[JPT][hapmap]
rs11085447	0.81[JPT][hapmap]
rs1114305	0.80[CHB][hapmap]
rs12974758	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12975081	0.85[JPT][hapmap]
rs12981564	0.80[JPT][hapmap]
rs12982282	0.80[JPT][hapmap]
rs13346641	0.86[CEU][hapmap]
rs1781867	0.95[CEU][hapmap]
rs1781872	0.95[CEU][hapmap]
rs1781873	0.81[JPT][hapmap]
rs1879234	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967182	0.90[CEU][hapmap]
rs2012013	0.81[JPT][hapmap]
rs2086319	0.84[JPT][hapmap]
rs2088762	0.81[JPT][hapmap]
rs2170024	0.81[JPT][hapmap]
rs2173727	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2359144	0.90[CEU][hapmap]
rs2359155	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562398	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562402	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs2562408	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562417	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562428	0.81[ASN][1000 genomes]
rs2562435	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs2562466	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562468	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562471	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562474	0.81[ASN][1000 genomes]
rs2562487	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2562507	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562508	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650773	0.83[ASN][1000 genomes]
rs2650784	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650792	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650793	0.90[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650798	0.85[JPT][hapmap]
rs2650801	0.82[ASN][1000 genomes]
rs2650804	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650805	0.95[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650814	0.83[ASN][1000 genomes]
rs2650819	0.83[ASN][1000 genomes]
rs2650825	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650844	0.90[CEU][hapmap]
rs2681377	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2681388	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2681389	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2681392	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2914626	0.80[CHB][hapmap]
rs2914638	0.81[JPT][hapmap]
rs2914645	0.85[JPT][hapmap]
rs2914646	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2928218	0.82[JPT][hapmap]
rs2937174	0.85[JPT][hapmap]
rs2946790	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968045	0.85[JPT][hapmap]
rs2968046	0.80[CHB][hapmap];0.94[CHD][hapmap]
rs2968076	0.85[ASN][1000 genomes]
rs2968078	0.83[ASN][1000 genomes]
rs2968082	0.80[CHB][hapmap]
rs35008138	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4315457	0.81[JPT][hapmap]
rs4321312	0.95[CEU][hapmap]
rs4359573	0.95[CEU][hapmap]
rs4524067	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4638726	0.90[CEU][hapmap]
rs472472	0.94[CHD][hapmap];0.80[JPT][hapmap]
rs4809145	0.92[CHB][hapmap]
rs489845	0.80[JPT][hapmap]
rs499445	0.92[CHD][hapmap];0.80[JPT][hapmap]
rs541639	0.89[CHD][hapmap];0.80[JPT][hapmap]
rs598959	0.80[JPT][hapmap]
rs600186	0.80[JPT][hapmap]
rs62110163	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs627522	0.95[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs6511239	0.80[JPT][hapmap]
rs6511250	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511253	0.95[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511254	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511256	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511258	0.90[AMR][1000 genomes]
rs7247411	0.81[JPT][hapmap]
rs7249412	0.81[JPT][hapmap]
rs7252261	0.81[JPT][hapmap]
rs7252585	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7257857	0.81[JPT][hapmap]
rs7259311	0.81[JPT][hapmap]
rs7260065	0.90[CEU][hapmap]
rs8099940	0.81[JPT][hapmap]
rs8103325	0.81[JPT][hapmap]
rs8103459	0.83[JPT][hapmap]
rs8106025	0.83[ASN][1000 genomes]
rs8110967	0.81[JPT][hapmap]
rs8112775	0.92[CHD][hapmap];0.80[JPT][hapmap]
rs924485	0.85[JPT][hapmap]
rs9304986	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9304987	0.91[AMR][1000 genomes];0.86[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	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

Variant related diseases (count:1)

Disease	PMID	Source
Pain	19207018	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2562456	ZNF738	cis	cerebellum	SCAN
rs2562456	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562456	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562456	ZNF43	cis	parietal	SCAN
rs2562456	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562456	ZNF708	cis	cerebellum	SCAN
rs2562456	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2562456	ZNF708	cis	Muscle Skeletal	GTEx
rs2562456	ZNF257	cis	parietal	SCAN
rs2562456	NCAN	cis	parietal	SCAN
rs2562456	ZNF708	cis	lung	GTEx
rs2562456	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562456	ZNF826P	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658200-21667400	Weak transcription	Right Atrium	heart
2	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
3	chr19:21659200-21668400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:21665400-21666400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:21665600-21666400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:21665600-21666400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr19:21665600-21666800	Active TSS	Osteobl	bone
8	chr19:21665600-21667000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
9	chr19:21665800-21666400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:21665800-21666400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr19:21665800-21666400	Active TSS	Colon Smooth Muscle	Colon
12	chr19:21665800-21666400	Active TSS	Rectal Smooth Muscle	rectum
13	chr19:21665800-21666600	ZNF genes & repeats	Thymus	Thymus
14	chr19:21665800-21666800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:21665800-21666800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
16	chr19:21665800-21666800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr19:21665800-21666800	Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr19:21665800-21666800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr19:21665800-21666800	Flanking Active TSS	Placenta	Placenta
20	chr19:21665800-21666800	ZNF genes & repeats	Lung	lung
21	chr19:21665800-21666800	Active TSS	Ovary	ovary
22	chr19:21665800-21667000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:21665800-21667000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:21666000-21666800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:21666000-21666800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:21666000-21666800	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr19:21666000-21666800	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:21666000-21668600	Weak transcription	Stomach Mucosa	stomach
29	chr19:21666200-21666400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr19:21666200-21666800	Active TSS	Primary B cells from peripheral blood	blood
31	chr19:21666200-21668400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:21666200-21668600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:21666200-21669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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