Variant report

Variant	rs35520457
Chromosome Location	chr19:56993984-56993985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12709959	0.86[AMR][1000 genomes]
rs12979827	0.89[AMR][1000 genomes]
rs17207432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17207481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28815239	0.86[AMR][1000 genomes]
rs34403290	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35215648	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36147582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121592	0.88[AMR][1000 genomes]
rs62121594	0.88[AMR][1000 genomes]
rs62121597	0.89[AMR][1000 genomes]
rs8113270	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749115	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35520457	MGC9913	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56990400-56994000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr19:56990400-56994200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:56990400-56996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr19:56990600-56994200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:56990800-57010000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:56991000-56998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:56991000-57005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:56991200-56994200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:56991200-56994600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:56991200-57001400	Weak transcription	Fetal Heart	heart
11	chr19:56991200-57006800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:56991200-57006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:56991600-56997600	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:56991600-56997800	ZNF genes & repeats	Ovary	ovary
15	chr19:56992000-57009400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
16	chr19:56992000-57009800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:56992400-56994200	Weak transcription	Fetal Stomach	stomach
18	chr19:56992400-56994200	Weak transcription	Left Ventricle	heart
19	chr19:56992400-57004800	Weak transcription	Right Ventricle	heart
20	chr19:56992600-56995000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:56992800-56994600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:56993400-56998000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:56993600-56994400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:56993600-56994600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
25	chr19:56993800-56994000	ZNF genes & repeats	Brain Anterior Caudate	brain

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