Variant report

Variant	rs8109617
Chromosome Location	chr19:56988039-56988040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56987970-56990186	IMR90	lung:	n/a	n/a
2	MAFK	chr19:56987985-56988391	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:56987914-56989927	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr19:56987837-56989882	H1-neurons	neurons:	n/a	n/a
5	MXI1	chr19:56987781-56990043	IMR90	lung:	n/a	n/a
6	MAZ	chr19:56987654-56990331	IMR90	lung:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
7	SIN3A	chr19:56988034-56990073	H1-hESC	embryonic stem cell:	n/a	chr19:56989351-56989364 chr19:56988699-56988708 chr19:56989198-56989209 chr19:56988812-56988823
8	REST	chr19:56987745-56989992	H1-neurons	neurons:	n/a	chr19:56989351-56989364
9	MXI1	chr19:56987494-56990858	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:56987976-56990044	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ZNF667	TF binding region
ZNF667-AS1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10409864	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10412888	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10425239	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425729	0.86[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261655	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509998	0.84[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251105	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253670	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253817	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254602	0.88[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7259359	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8108715	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[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	esv3358424	chr19:56987565-56990113	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8109617	ZNF460	cis	parietal	SCAN
rs8109617	ZNF667	cis	Esophagus Muscularis	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56985400-56990400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:56985400-56991400	ZNF genes & repeats	Liver	Liver
3	chr19:56987000-56990000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56987000-56990400	ZNF genes & repeats	Gastric	stomach
5	chr19:56987400-56988200	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr19:56987400-56988400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:56987400-56988400	Flanking Active TSS	Dnd41	blood
8	chr19:56987400-56988600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
9	chr19:56987400-56988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:56987400-56990000	ZNF genes & repeats	Placenta	Placenta
11	chr19:56987400-56990800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:56987400-56992400	ZNF genes & repeats	Lung	lung
13	chr19:56987600-56988200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr19:56987600-56988200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:56987600-56988200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:56987600-56988200	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr19:56987600-56988200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:56987600-56988200	Flanking Active TSS	Fetal Brain Male	brain
19	chr19:56987600-56988200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:56987600-56988400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr19:56987600-56988400	Flanking Active TSS	Fetal Lung	lung
22	chr19:56987600-56988600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr19:56987600-56988600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:56987600-56989600	ZNF genes & repeats	Pancreas	Pancrea
25	chr19:56987600-56989800	Active TSS	Primary T cells from cord blood	blood
26	chr19:56987600-56990200	ZNF genes & repeats	Spleen	Spleen
27	chr19:56987600-56990600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:56987600-56990600	Active TSS	Brain Anterior Caudate	brain
29	chr19:56987600-56990800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr19:56987600-56990800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr19:56987600-56991000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:56987600-56991200	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr19:56987800-56988200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:56987800-56988200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr19:56987800-56988200	Flanking Active TSS	Fetal Heart	heart
36	chr19:56987800-56988200	Flanking Active TSS	Fetal Kidney	kidney
37	chr19:56987800-56988400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr19:56987800-56988400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:56987800-56988400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:56987800-56988400	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr19:56987800-56988400	Flanking Active TSS	Fetal Stomach	stomach
42	chr19:56987800-56988400	Flanking Active TSS	Ovary	ovary
43	chr19:56987800-56988400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr19:56987800-56988400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr19:56987800-56988600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr19:56987800-56988600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr19:56987800-56989800	Active TSS	Osteobl	bone
48	chr19:56987800-56990000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:56987800-56990200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:56987800-56990400	Active TSS	HUES48 Cell Line	embryonic stem cell

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