Variant report

Variant	rs12461029
Chromosome Location	chr19:18220312-18220313
allele	A/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	ESRRA	chr19:18220092-18220788	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:18220106-18221084	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:18220018-18221076	HepG2	liver:	n/a	n/a
4	MXI1	chr19:18220125-18220411	HepG2	liver:	n/a	n/a
5	TAF1	chr19:18220093-18221091	HepG2	liver:	n/a	n/a
6	CEBPD	chr19:18220216-18220940	HepG2	liver:	n/a	n/a
7	MTA3	chr19:18219785-18220612	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:18220074-18220980	HepG2	liver:	n/a	n/a
9	HEY1	chr19:18219965-18221170	HepG2	liver:	n/a	chr19:18220909-18220924 chr19:18220972-18220987 chr19:18220917-18220932 chr19:18220766-18220781
10	MAX	chr19:18219929-18221443	HepG2	liver:	n/a	chr19:18221239-18221248 chr19:18221189-18221199 chr19:18221312-18221322
11	HNF4A	chr19:18220025-18220830	HepG2	liver:	n/a	chr19:18220256-18220271 chr19:18220257-18220270 chr19:18220710-18220725 chr19:18220255-18220270 chr19:18220256-18220271 chr19:18220257-18220269 chr19:18220257-18220269 chr19:18220256-18220271
12	MBD4	chr19:18220173-18220544	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:18219935-18221387	HepG2	liver:	n/a	n/a
14	HNF4G	chr19:18219681-18220639	HepG2	liver:	n/a	chr19:18220256-18220271 chr19:18220257-18220270 chr19:18220256-18220271 chr19:18220257-18220269 chr19:18220257-18220269 chr19:18220256-18220271
15	MYBL2	chr19:18219985-18220522	HepG2	liver:	n/a	n/a
16	RCOR1	chr19:18220115-18220485	HepG2	liver:	n/a	n/a
17	MAZ	chr19:18220284-18221639	IMR90	lung:	n/a	chr19:18221568-18221578 chr19:18221239-18221248 chr19:18221189-18221199 chr19:18221312-18221322
18	MAFK	chr19:18220276-18220460	HepG2	liver:	n/a	n/a
19	HEY1	chr19:18219935-18220973	HepG2	liver:	n/a	chr19:18220909-18220924 chr19:18220917-18220932 chr19:18220766-18220781
20	CEBPB	chr19:18220230-18220928	HepG2	liver:	n/a	chr19:18220754-18220765
21	TBP	chr19:18220169-18220386	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:18219926-18221099	HepG2	liver:	n/a	n/a
23	ZBTB7A	chr19:18220211-18221739	ECC-1	luminal epithelium:	n/a	chr19:18221416-18221423
24	ELF1	chr19:18220170-18221326	GM12878	blood:	n/a	chr19:18220829-18220841 chr19:18221274-18221286 chr19:18221278-18221287 chr19:18220898-18220907
25	ZBTB7A	chr19:18220300-18221744	ECC-1	luminal epithelium:	n/a	chr19:18221416-18221423
26	HNF4A	chr19:18220002-18220526	HepG2	liver:	n/a	chr19:18220256-18220271 chr19:18220257-18220270 chr19:18220255-18220270 chr19:18220256-18220271 chr19:18220257-18220269 chr19:18220257-18220269 chr19:18220256-18220271
27	ZBTB7A	chr19:18220028-18220490	HepG2	liver:	n/a	n/a
28	NFIC	chr19:18220139-18220819	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:18219953-18221019	HepG2	liver:	n/a	n/a
30	HNF4G	chr19:18220035-18220791	HepG2	liver:	n/a	chr19:18220256-18220271 chr19:18220257-18220270 chr19:18220256-18220271 chr19:18220257-18220269 chr19:18220257-18220269 chr19:18220256-18220271
31	MYBL2	chr19:18219936-18220491	HepG2	liver:	n/a	n/a
32	HNF4A	chr19:18220059-18220706	HepG2	liver:	n/a	chr19:18220256-18220271 chr19:18220257-18220270 chr19:18220255-18220270 chr19:18220256-18220271 chr19:18220257-18220269 chr19:18220257-18220269 chr19:18220256-18220271
33	CHD2	chr19:18220055-18220492	HepG2	liver:	n/a	n/a
34	POLR2A	chr19:18220132-18220887	HepG2	liver:	n/a	n/a
35	EP300	chr19:18220116-18220381	HepG2	liver:	n/a	n/a
36	ZNF263	chr19:18220286-18220557	HEK293-T-REx	kidney:	n/a	chr19:18220414-18220423
37	ARID3A	chr19:18220134-18220398	HepG2	liver:	n/a	n/a
38	SP1	chr19:18220007-18220893	HepG2	liver:	n/a	n/a
39	HDAC2	chr19:18220042-18220461	HepG2	liver:	n/a	chr19:18220268-18220276
40	TAF1	chr19:18219994-18221267	HepG2	liver:	n/a	n/a
41	MAZ	chr19:18220093-18221088	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18212757..18214492-chr19:18218633..18220629,2	MCF-7	breast:
2	chr19:18207114..18212211-chr19:18216815..18222515,8	K562	blood:
3	chr19:18218520..18220577-chr19:18390459..18392141,2	K562	blood:
4	chr19:18218465..18220344-chr19:18262421..18265110,2	MCF-7	breast:
5	chr19:18220149..18221787-chr19:18528170..18529964,2	K562	blood:
6	chr19:18206855..18210303-chr19:18216702..18222515,7	K562	blood:
7	chr19:18218810..18222219-chr19:18263257..18265639,4	K562	blood:
8	chr19:18060053..18061688-chr19:18218502..18220719,2	K562	blood:
9	chr19:18219638..18222219-chr19:18263591..18265639,2	K562	blood:

Variant related genes	Relation type
MAST3	TF binding region
ENSG00000268173	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000096996	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000130522	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11086090	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11086092	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11086093	0.80[EUR][1000 genomes]
rs12052062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459449	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12460262	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12460575	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12462442	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12609740	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12610206	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12611216	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3826967	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs45492191	0.85[AMR][1000 genomes]
rs60963202	0.86[EUR][1000 genomes]
rs62121152	0.82[EUR][1000 genomes]
rs62121153	0.86[EUR][1000 genomes]
rs62121154	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62123563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123565	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62123566	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62123567	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62123569	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62123598	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62123599	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62123601	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123602	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62123603	0.84[EUR][1000 genomes]
rs62123604	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62123605	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62123606	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62123608	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs740692	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs740693	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18215600-18220400	Weak transcription	Esophagus	oesophagus
2	chr19:18215600-18220400	Weak transcription	Lung	lung
3	chr19:18215800-18220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:18215800-18220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:18215800-18220400	Enhancers	Primary B cells from peripheral blood	blood
6	chr19:18215800-18220400	Weak transcription	Primary T cells from cord blood	blood
7	chr19:18215800-18220400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:18215800-18220400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:18215800-18220400	Weak transcription	Fetal Heart	heart
10	chr19:18215800-18220400	Weak transcription	Ovary	ovary
11	chr19:18215800-18220400	Weak transcription	HMEC	breast
12	chr19:18215800-18220400	Weak transcription	HSMM	muscle
13	chr19:18215800-18220400	Weak transcription	NHLF	lung
14	chr19:18215800-18220400	Weak transcription	Osteobl	bone
15	chr19:18215800-18220600	Enhancers	Primary B cells from cord blood	blood
16	chr19:18216000-18220400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:18216000-18220400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:18216000-18220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:18216000-18220600	Weak transcription	Aorta	Aorta
20	chr19:18218000-18220400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr19:18218000-18220400	Enhancers	Fetal Thymus	thymus
22	chr19:18218000-18220600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:18218200-18220400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:18218200-18220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:18219200-18220400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr19:18219400-18220400	Enhancers	K562	blood
27	chr19:18219600-18220400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr19:18219600-18220400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:18219600-18220400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:18219600-18220400	Enhancers	Brain Substantia Nigra	brain
31	chr19:18219600-18220400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
32	chr19:18219600-18220600	Enhancers	Gastric	stomach
33	chr19:18219600-18220600	Flanking Active TSS	A549	lung
34	chr19:18219600-18220800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr19:18219600-18221000	Enhancers	Stomach Mucosa	stomach
36	chr19:18219800-18220400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:18219800-18220400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr19:18219800-18220400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:18219800-18220400	Enhancers	Brain Anterior Caudate	brain
40	chr19:18219800-18220400	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr19:18219800-18220400	Enhancers	Placenta	Placenta
42	chr19:18219800-18220400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
43	chr19:18219800-18220600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr19:18219800-18220600	Flanking Active TSS	Liver	Liver
45	chr19:18219800-18220600	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr19:18219800-18220600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr19:18219800-18220600	Enhancers	Spleen	Spleen
48	chr19:18219800-18220600	Flanking Active TSS	Hela-S3	cervix
49	chr19:18219800-18221200	Active TSS	Rectal Smooth Muscle	rectum
50	chr19:18219800-18222000	Flanking Active TSS	Colonic Mucosa	Colon

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