Variant report

Variant	rs12460575
Chromosome Location	chr19:18229907-18229908
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZEB1	chr19:18229863-18230430	GM12878	blood:	n/a	chr19:18230187-18230196 chr19:18230153-18230162 chr19:18230154-18230161 chr19:18230188-18230195
2	MAZ	chr19:18228174-18230196	IMR90	lung:	n/a	chr19:18229136-18229145 chr19:18228875-18228885
3	POLR2A	chr19:18229870-18229915	HepG2	liver:	n/a	n/a
4	MTA3	chr19:18229467-18230651	GM12878	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18214257..18217360-chr19:18228399..18230348,3	MCF-7	breast:
2	chr19:18219845..18222169-chr19:18228682..18230184,2	K562	blood:
3	chr19:18227326..18231361-chr19:18269226..18272590,3	MCF-7	breast:
4	chr19:18228709..18231105-chr19:18284369..18286755,2	MCF-7	breast:
5	chr19:18226813..18230040-chr19:18231036..18235239,5	MCF-7	breast:
6	chr19:18227630..18230572-chr19:18230965..18237088,9	K562	blood:
7	chr19:18227532..18230365-chr19:18238689..18243029,3	K562	blood:
8	chr19:18057341..18060009-chr19:18227603..18230383,4	K562	blood:
9	chr19:18226626..18231621-chr19:18270177..18272430,5	K562	blood:
10	chr19:18208981..18212073-chr19:18226355..18230171,3	K562	blood:
11	chr19:18227762..18230364-chr19:18242622..18244153,2	K562	blood:
12	chr19:18228665..18230746-chr19:18250614..18253452,2	MCF-7	breast:
13	chr19:18228264..18231141-chr19:18383413..18385750,2	K562	blood:
14	chr19:18228257..18230601-chr19:18266125..18268282,4	MCF-7	breast:
15	chr19:18226689..18233128-chr19:18261137..18272674,17	K562	blood:
16	chr19:18228276..18230245-chr19:18234109..18236179,2	MCF-7	breast:
17	chr19:18223950..18226906-chr19:18227194..18230547,6	K562	blood:
18	chr19:18226691..18231532-chr19:18258960..18265353,9	MCF-7	breast:
19	chr19:18226427..18233128-chr19:18260600..18269360,14	K562	blood:
20	chr19:18228746..18230484-chr19:18244815..18246440,2	K562	blood:

No data

Variant related genes	Relation type
MAST3	TF binding region
ENSG00000096996	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000130518	Chromatin interaction
ENSG00000216490	Chromatin interaction
ENSG00000099308	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11086090	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11086092	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11086093	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12052062	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459449	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460262	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12461029	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12462442	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12609740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12610206	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12611216	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3826967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs45492191	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60963202	0.83[EUR][1000 genomes]
rs62121153	0.83[EUR][1000 genomes]
rs62121154	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62123563	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62123564	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62123565	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123566	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123567	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62123569	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123598	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62123599	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62123601	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62123602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62123603	0.87[EUR][1000 genomes]
rs62123604	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62123605	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62123606	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62123608	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs740692	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740693	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	esv1834142	chr19:18224729-18234588	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
20	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18228000-18230200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:18228200-18230600	Flanking Active TSS	HMEC	breast
3	chr19:18228600-18230600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:18228800-18230400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:18228800-18230800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr19:18229000-18230000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr19:18229000-18230000	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr19:18229000-18230000	Flanking Active TSS	Colonic Mucosa	Colon
9	chr19:18229000-18230000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr19:18229000-18230000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr19:18229000-18230200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:18229000-18230200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr19:18229000-18230200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:18229000-18230200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:18229000-18230200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:18229000-18230200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr19:18229000-18230200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr19:18229000-18230400	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr19:18229000-18230600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr19:18229000-18230600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr19:18229000-18230600	Flanking Active TSS	Fetal Thymus	thymus
22	chr19:18229000-18230600	Flanking Active TSS	Dnd41	blood
23	chr19:18229000-18231000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:18229000-18231000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:18229000-18231000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr19:18229000-18231000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:18229000-18231000	Flanking Active TSS	GM12878-XiMat	blood
28	chr19:18229200-18230000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr19:18229200-18230000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:18229200-18230000	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr19:18229200-18230000	Flanking Active TSS	Hela-S3	cervix
32	chr19:18229200-18230000	Flanking Active TSS	HepG2	liver
33	chr19:18229200-18230200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:18229200-18230200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:18229200-18230200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:18229200-18230200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:18229200-18230200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:18229200-18230200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr19:18229200-18230200	Flanking Active TSS	NHLF	lung
40	chr19:18229200-18230400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:18229200-18230400	Flanking Active TSS	Thymus	Thymus
42	chr19:18229200-18230600	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr19:18229200-18230600	Flanking Active TSS	Fetal Brain Female	brain
44	chr19:18229200-18230800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:18229200-18230800	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:18229200-18230800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:18229200-18231000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr19:18229200-18231000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:18229200-18231000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:18229200-18231000	Enhancers	Spleen	Spleen

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