Variant report

Variant	rs12460170
Chromosome Location	chr19:53669492-53669493
allele	A/G
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	SETDB1	chr19:53667859-53670059	K562	blood:	n/a	n/a
2	ZNF274	chr19:53667870-53669777	H1-hESC	embryonic stem cell:	n/a	n/a
3	KAP1	chr19:53668154-53669837	K562	blood:	n/a	n/a
4	ZNF274	chr19:53667705-53670265	K562	blood:	n/a	n/a
5	ZNF274	chr19:53668791-53669564	GM12878	blood:	n/a	n/a
6	ZNF274	chr19:53667843-53669570	K562	blood:	n/a	n/a
7	POLR2A	chr19:53669474-53670089	K562	blood:	n/a	n/a
8	ZNF274	chr19:53668262-53669619	NT2-D1	testis:	n/a	n/a
9	ZNF274	chr19:53668237-53669599	GM08714	blood:	n/a	n/a

Variant related genes	Relation type
ZNF665	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10454108	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084221	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11084222	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1133145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670027	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12459469	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461724	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12971799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971840	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975164	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34751425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801961	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803054	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803055	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62115530	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115533	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6509728	0.91[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73057882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101962	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8112056	0.89[EUR][1000 genomes]
rs8112368	0.88[EUR][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	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
9	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv912350	chr19:53636016-53687818	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv912351	chr19:53655493-53702508	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv580077	chr19:53664448-53669492	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2762999	chr19:53665818-53709353	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12460170	ZNF347	cis	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53664400-53670200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:53664800-53695400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:53666600-53670400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:53666800-53669600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53667000-53669800	ZNF genes & repeats	Brain Hippocampus Middle	brain
6	chr19:53667000-53670000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:53667000-53670200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:53667000-53670400	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:53667200-53670200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:53667600-53669600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:53667600-53669600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:53667600-53669600	ZNF genes & repeats	Ovary	ovary
13	chr19:53667600-53670000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
14	chr19:53667600-53670200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:53667800-53669600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr19:53667800-53669600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:53667800-53669600	ZNF genes & repeats	Fetal Lung	lung
18	chr19:53667800-53669600	ZNF genes & repeats	Left Ventricle	heart
19	chr19:53667800-53670000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:53667800-53670600	ZNF genes & repeats	Dnd41	blood
21	chr19:53668000-53669600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:53668000-53669600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:53668000-53669600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr19:53668000-53669600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
25	chr19:53668000-53669600	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr19:53668000-53669800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr19:53668000-53669800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:53668000-53669800	ZNF genes & repeats	Colon Smooth Muscle	Colon
29	chr19:53668000-53670000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr19:53668000-53670000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:53668200-53669600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:53668200-53669600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr19:53668200-53669600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:53668200-53669600	ZNF genes & repeats	Brain Substantia Nigra	brain
35	chr19:53668200-53669600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
36	chr19:53668200-53669600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
37	chr19:53668200-53669600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
38	chr19:53668200-53669600	ZNF genes & repeats	NHDF-Ad	bronchial
39	chr19:53668200-53669800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr19:53668200-53669800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
41	chr19:53668200-53670600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr19:53668400-53669600	ZNF genes & repeats	Aorta	Aorta
43	chr19:53668400-53669600	ZNF genes & repeats	Osteobl	bone
44	chr19:53668400-53670000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
45	chr19:53668400-53670000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:53668400-53670200	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr19:53668600-53669600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:53668600-53669600	ZNF genes & repeats	Colonic Mucosa	Colon
49	chr19:53668600-53669600	ZNF genes & repeats	Fetal Brain Male	brain
50	chr19:53668800-53669600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin

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