Variant report

Variant	rs2061915
Chromosome Location	chr19:21459033-21459034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-5	chr19:21458825-21459134	NONHSAT063694

Extended variants
information (count: 31 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10402151	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409412	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1080829	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085441	0.88[ASW][hapmap];0.91[YRI][hapmap]
rs11085447	0.88[ASW][hapmap]
rs12975081	0.88[ASW][hapmap]
rs2012013	0.82[ASW][hapmap]
rs2022513	0.85[ASN][1000 genomes]
rs2080068	0.85[ASN][1000 genomes]
rs2088762	0.88[ASW][hapmap]
rs2192082	0.84[ASN][1000 genomes]
rs279797	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4315457	0.88[ASW][hapmap]
rs7247411	0.83[ASW][hapmap]
rs7250918	0.83[ASN][1000 genomes]
rs7252261	0.88[ASW][hapmap]
rs7252759	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7254094	0.84[MEX][hapmap]
rs7508671	0.81[CEU][hapmap]
rs8103325	0.88[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs2061915	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs2061915	ZNF429	cis	multi-tissue	Pritchard
rs2061915	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs2061915	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs2061915	RP11-678G14.2	cis	lung	GTEx
rs2061915	ELL	cis	parietal	SCAN
rs2061915	LRRC25	cis	parietal	SCAN
rs2061915	ZNF100	cis	cerebellum	SCAN
rs2061915	ZNF708	cis	cerebellum	SCAN
rs2061915	ZNF738	cis	parietal	SCAN
rs2061915	NDUFA13	cis	cerebellum	SCAN
rs2061915	ZNF208	cis	parietal	SCAN
rs2061915	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs2061915	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2061915	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2061915	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs2061915	IL12RB1	cis	parietal	SCAN
rs2061915	TMEM59L	cis	parietal	SCAN
rs2061915	ZNF493	cis	cerebellum	SCAN
rs2061915	CTD-2561J22.5	cis	lung	GTEx
rs2061915	RP11-678G14.2	cis	Thyroid	GTEx
rs2061915	ZNF493	cis	multi-tissue	Pritchard
rs2061915	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs2061915	ZNF493	cis	Lymphoblastoid	GTEx
rs2061915	ZNF429	cis	cerebellum	SCAN
rs2061915	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21458600-21461200	ZNF genes & repeats	Liver	Liver
2	chr19:21458800-21459600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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