Variant report

Variant	rs2562428
Chromosome Location	chr19:21625454-21625455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12974758	0.80[ASN][1000 genomes]
rs2562398	0.83[AFR][1000 genomes]
rs2562417	0.90[AFR][1000 genomes]
rs2562456	0.81[ASN][1000 genomes]
rs2562474	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562487	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562507	0.90[AFR][1000 genomes]
rs2562508	0.90[AFR][1000 genomes]
rs2650764	0.85[ASN][1000 genomes]
rs2650773	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650784	0.81[ASN][1000 genomes]
rs2650801	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650805	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2650814	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650819	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2681370	0.81[AFR][1000 genomes]
rs2681388	0.90[AFR][1000 genomes]
rs2914646	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928211	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2946790	0.90[AFR][1000 genomes]
rs2968072	0.87[ASN][1000 genomes]
rs2968076	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968078	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35008138	0.90[AFR][1000 genomes]
rs35099594	0.90[AFR][1000 genomes]
rs56072098	0.90[ASN][1000 genomes]
rs58001930	0.81[AFR][1000 genomes]
rs62110163	0.90[AFR][1000 genomes]
rs62110205	0.81[AFR][1000 genomes]
rs6511250	0.87[ASN][1000 genomes]
rs6511256	0.90[AFR][1000 genomes]
rs7252585	0.82[ASN][1000 genomes]
rs8106025	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304986	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2562428	ZNF708	cis	lung	GTEx
rs2562428	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562428	ZNF708	cis	Muscle Skeletal	GTEx
rs2562428	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:21618200-21626800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:21622400-21632600	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:21623200-21630400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21623400-21626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:21623600-21625600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr19:21623800-21625600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr19:21624200-21626400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:21624600-21636400	Weak transcription	Fetal Kidney	kidney
10	chr19:21625000-21625600	Strong transcription	Dnd41	blood
11	chr19:21625000-21625800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr19:21625000-21625800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:21625200-21625600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr19:21625200-21625600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr19:21625400-21625600	Enhancers	Ovary	ovary

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