Variant report

Variant	rs877394
Chromosome Location	chr19:57002137-57002138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10404345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404523	0.86[JPT][hapmap]
rs10408147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408921	0.86[JPT][hapmap]
rs10413986	0.85[JPT][hapmap]
rs10423274	0.86[JPT][hapmap]
rs10426952	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974540	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17273400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17273407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35558315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35967838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760848	0.86[JPT][hapmap]
rs60141587	0.81[AFR][1000 genomes]
rs8112950	0.85[JPT][hapmap]
rs877395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877394	ZNF460	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56990800-57010000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:56991000-57005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:56991200-57006800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:56991200-57006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:56992000-57009400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
6	chr19:56992000-57009800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:56992400-57004800	Weak transcription	Right Ventricle	heart
8	chr19:56996400-57005200	Weak transcription	Fetal Stomach	stomach
9	chr19:56998600-57003600	ZNF genes & repeats	Ovary	ovary
10	chr19:56998600-57008800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr19:56999600-57005400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:56999800-57006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:57001000-57005600	Weak transcription	HSMM	muscle
14	chr19:57001200-57003200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:57001400-57003600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr19:57001400-57003800	Enhancers	Fetal Heart	heart
17	chr19:57001600-57002200	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr19:57001800-57002200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr19:57001800-57002200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:57001800-57002200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
21	chr19:57001800-57003000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:57001800-57003200	ZNF genes & repeats	Brain Hippocampus Middle	brain
23	chr19:57001800-57005800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr19:57002000-57002200	Enhancers	Left Ventricle	heart
25	chr19:57002000-57002600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr19:57002000-57002600	Enhancers	HSMMtube	muscle
27	chr19:57002000-57003000	Enhancers	H1 Cell Line	embryonic stem cell

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