Variant report

Variant	rs7247623
Chromosome Location	chr19:21392852-21392853
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12973927	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1988919	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2358963	0.82[EUR][1000 genomes]
rs279797	0.83[CHB][hapmap]
rs29707	0.80[ASN][1000 genomes]
rs29708	0.80[ASN][1000 genomes]
rs39578	0.80[ASN][1000 genomes]
rs7248106	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259257	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259809	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101643	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8111817	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8111954	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9749580	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv911414	chr19:21355473-21454672	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2762988	chr19:21384837-21400142	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	nsv911418	chr19:21390608-21454672	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv517759	chr19:21391844-21420882	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7247623	ZNF429	cis	cerebellum	SCAN
rs7247623	NDUFA13	cis	cerebellum	SCAN
rs7247623	ZNF493	cis	Lymphoblastoid	GTEx
rs7247623	LRRC25	cis	parietal	SCAN
rs7247623	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7247623	ELL	cis	parietal	SCAN
rs7247623	ZNF208	cis	parietal	SCAN
rs7247623	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7247623	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7247623	ZNF429	cis	multi-tissue	Pritchard
rs7247623	ZNF738	cis	parietal	SCAN
rs7247623	ZNF493	cis	multi-tissue	Pritchard
rs7247623	ZNF493	cis	cerebellum	SCAN
rs7247623	IL12RB1	cis	parietal	SCAN
rs7247623	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21389600-21397600	Weak transcription	Ovary	ovary
2	chr19:21392800-21393000	Enhancers	HepG2	liver
3	chr19:21392800-21393600	Enhancers	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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