Variant report

Variant	rs2562487
Chromosome Location	chr19:21651382-21651383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10420016	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1055753	0.81[JPT][hapmap]
rs11085441	0.82[JPT][hapmap]
rs11085447	0.81[JPT][hapmap]
rs1114305	0.93[CHB][hapmap]
rs12974758	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12975081	0.85[JPT][hapmap]
rs12981564	0.80[JPT][hapmap]
rs12982282	0.80[JPT][hapmap]
rs1781867	0.95[CEU][hapmap]
rs1781872	0.94[CEU][hapmap]
rs1781873	0.81[JPT][hapmap]
rs1967182	0.81[CEU][hapmap]
rs2012013	0.81[JPT][hapmap]
rs2086319	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2088762	0.81[JPT][hapmap]
rs2170024	0.81[JPT][hapmap]
rs2173727	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2359144	0.81[CEU][hapmap]
rs2562398	0.83[AFR][1000 genomes]
rs2562402	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs2562408	0.81[AMR][1000 genomes]
rs2562417	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2562428	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562435	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs2562456	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2562466	0.81[AMR][1000 genomes]
rs2562468	0.81[AMR][1000 genomes]
rs2562471	0.81[AMR][1000 genomes]
rs2562474	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562507	0.90[AFR][1000 genomes]
rs2562508	0.90[AFR][1000 genomes]
rs2650764	0.81[ASN][1000 genomes]
rs2650773	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650784	0.85[ASN][1000 genomes]
rs2650792	0.80[ASN][1000 genomes]
rs2650793	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2650798	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2650801	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650804	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2650805	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2650814	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650819	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650825	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681370	0.81[AFR][1000 genomes]
rs2681377	0.81[AMR][1000 genomes]
rs2681388	0.90[AFR][1000 genomes]
rs2681389	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681392	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914626	0.93[CHB][hapmap]
rs2914638	0.81[JPT][hapmap]
rs2914645	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2914646	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928211	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2928218	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2937174	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2946790	0.90[AFR][1000 genomes]
rs2968045	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2968046	0.93[CHB][hapmap];0.94[CHD][hapmap]
rs2968072	0.87[ASN][1000 genomes]
rs2968076	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968078	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968082	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs35008138	0.90[AFR][1000 genomes]
rs35099594	0.90[AFR][1000 genomes]
rs4315457	0.81[JPT][hapmap]
rs4321312	0.95[CEU][hapmap]
rs4359573	0.95[CEU][hapmap]
rs4638726	0.85[CEU][hapmap]
rs472472	0.86[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs4809145	0.92[CHB][hapmap]
rs489845	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs499445	0.86[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap]
rs501563	0.92[CHB][hapmap]
rs541639	0.86[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap]
rs56072098	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58001930	0.81[AFR][1000 genomes]
rs598959	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs600186	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs62110163	0.90[AFR][1000 genomes]
rs62110205	0.81[AFR][1000 genomes]
rs627522	0.95[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs6511239	0.80[JPT][hapmap]
rs6511250	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511253	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6511254	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6511256	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6511258	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7247411	0.81[JPT][hapmap]
rs7249412	0.81[JPT][hapmap]
rs7252261	0.81[JPT][hapmap]
rs7252585	0.85[ASN][1000 genomes]
rs7257857	0.81[JPT][hapmap]
rs7259311	0.81[JPT][hapmap]
rs7260065	0.89[CEU][hapmap]
rs8099940	0.81[JPT][hapmap]
rs8103325	0.81[JPT][hapmap]
rs8103459	0.83[JPT][hapmap]
rs8106025	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110967	0.81[JPT][hapmap]
rs8112775	0.86[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap]
rs924485	0.85[JPT][hapmap]
rs9304986	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9304987	0.82[AMR][1000 genomes];0.82[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2562487	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562487	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562487	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562487	ZNF708	cis	Muscle Skeletal	GTEx
rs2562487	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2562487	PDE4C	cis	cerebellum	SCAN
rs2562487	ZNF708	cis	lung	GTEx
rs2562487	ZNF738	cis	cerebellum	SCAN
rs2562487	ZNF43	cis	parietal	SCAN
rs2562487	ZNF708	cis	cerebellum	SCAN
rs2562487	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562487	ZNF493	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21647000-21657200	Weak transcription	Right Atrium	heart
2	chr19:21647200-21651600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:21648800-21651800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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