Variant report

Variant	rs12462708
Chromosome Location	chr19:37797578-37797579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10419281	1.00[ASW][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11083420	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666708	0.82[ASN][1000 genomes]
rs12462487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1545755	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs185368	0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs185369	0.81[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1968251	0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.83[MKK][hapmap]
rs2385180	0.82[ASW][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2385181	0.82[ASN][1000 genomes]
rs2431992	0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs256733	0.82[ASW][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs256735	0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs256740	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256744	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2921561	0.81[EUR][1000 genomes]
rs320881	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs320887	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs502546	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55755939	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55926714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254009	1.00[ASW][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs7257354	0.84[EUR][1000 genomes]
rs73025481	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8109103	0.82[ASW][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs862234	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]

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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
4	esv3520361	chr19:37745067-37811325	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3520362	chr19:37745067-37811325	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv978811	chr19:37749967-37820517	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
8	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs12462708	DMPK	cis	parietal	SCAN
rs12462708	AC012309.5	cis	Esophagus Muscularis	GTEx
rs12462708	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12462708	SIPA1L3	cis	cerebellum	SCAN
rs12462708	ARHGEF1	cis	cerebellum	SCAN
rs12462708	ZNF585B	cis	Artery Tibial	GTEx
rs12462708	AC012309.5	cis	Heart Left Ventricle	GTEx
rs12462708	PAK4	cis	cerebellum	SCAN
rs12462708	CCDC97	cis	cerebellum	SCAN
rs12462708	LINC00665	cis	Heart Left Ventricle	GTEx
rs12462708	KIAA0961	cis	multi-tissue	Pritchard
rs12462708	AC012309.5	cis	Adipose Subcutaneous	GTEx
rs12462708	POU2F2	cis	parietal	SCAN
rs12462708	AC012309.5	cis	Thyroid	GTEx
rs12462708	HKR1	cis	Whole Blood	GTEx
rs12462708	AC012309.5	cis	Muscle Skeletal	GTEx
rs12462708	AC012309.5	cis	Esophagus Mucosa	GTEx
rs12462708	IL29	cis	parietal	SCAN
rs12462708	PVR	cis	parietal	SCAN
rs12462708	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs12462708	ZNF781	cis	Thyroid	GTEx
rs12462708	HIPK4	cis	parietal	SCAN
rs12462708	HKR1	cis	multi-tissue	Pritchard
rs12462708	AC012309.5	cis	Artery Tibial	GTEx
rs12462708	PLEKHG2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37794400-37798400	ZNF genes & repeats	Fetal Brain Female	brain
2	chr19:37796000-37801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:37797400-37797600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell

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