Variant report

Variant	rs12459918
Chromosome Location	chr19:55857123-55857124
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	MAZ	chr19:55856790-55857557	Hela-S3	cervix:	n/a	chr19:55857211-55857221
2	POLR2A	chr19:55855730-55858044	K562	blood:	n/a	n/a
3	POLR2A	chr19:55856948-55857301	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr19:55856844-55857631	ECC-1	luminal epithelium:	n/a	chr19:55857269-55857285 chr19:55857269-55857286
5	POLR2A	chr19:55855879-55857185	K562	blood:	n/a	n/a
6	POLR2A	chr19:55856792-55857419	K562	blood:	n/a	n/a
7	SMC3	chr19:55857115-55857493	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr19:55856935-55857537	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr19:55856951-55857482	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:55856762-55857537	Hela-S3	cervix:	n/a	n/a
11	EGR1	chr19:55856935-55857408	ECC-1	luminal epithelium:	n/a	chr19:55857155-55857168 chr19:55857157-55857167 chr19:55857155-55857168 chr19:55857158-55857168 chr19:55857151-55857173 chr19:55857155-55857168 chr19:55857158-55857167 chr19:55857156-55857167 chr19:55857155-55857168
12	POLR2A	chr19:55856726-55858064	K562	blood:	n/a	n/a
13	POLR2A	chr19:55857010-55857453	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr19:55857096-55857127	HepG2	liver:	n/a	n/a
15	BCL3	chr19:55857016-55857597	A549	lung:	n/a	n/a
16	POLR2A	chr19:55857056-55857332	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:55857012-55857366	Hela-S3	cervix:	n/a	n/a
18	NFIC	chr19:55856830-55857679	ECC-1	luminal epithelium:	n/a	chr19:55857269-55857285 chr19:55857269-55857286
19	CHD2	chr19:55857060-55857477	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:55857092-55857374	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:55856967-55857537	Hela-S3	cervix:	n/a	n/a
22	MAX	chr19:55857121-55857464	Hela-S3	cervix:	n/a	chr19:55857211-55857221
23	HMGN3	chr19:55856977-55857177	K562	blood:	n/a	n/a
24	POLR2A	chr19:55856881-55857268	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55769670..55772442-chr19:55857047..55859778,2	K562	blood:
2	chr19:55855835..55857937-chr19:55888038..55890020,2	K562	blood:
3	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
4	chr19:55856384..55859080-chr19:55879922..55882670,2	K562	blood:
5	chr19:55853165..55857260-chr19:55879821..55883048,3	MCF-7	breast:
6	chr19:55855397..55858680-chr19:55917740..55920273,3	K562	blood:
7	chr19:55855203..55857360-chr19:55872497..55875257,2	MCF-7	breast:
8	chr19:55854922..55862011-chr19:55892906..55898744,13	MCF-7	breast:

Variant related genes	Relation type
SUV420H2	TF binding region
ENSG00000160472	Chromatin interaction
ENSG00000269275	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000180043	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10405231	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1058511	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11084395	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription 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	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers 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 miRNA target site	203 gene(s)	inside rSNPs	diseases
13	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
14	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
15	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55852400-55860200	Weak transcription	Aorta	Aorta
2	chr19:55852600-55857400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:55852800-55857400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:55852800-55859600	Weak transcription	Psoas Muscle	Psoas
5	chr19:55853200-55857400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:55853200-55857600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr19:55853200-55857600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:55853200-55859600	Weak transcription	Fetal Kidney	kidney
9	chr19:55853200-55859800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr19:55853200-55860400	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr19:55853200-55860400	Genic enhancers	Fetal Muscle Leg	muscle
12	chr19:55853200-55861400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:55853200-55861800	Weak transcription	Small Intestine	intestine
14	chr19:55853200-55861800	Weak transcription	NHEK	skin
15	chr19:55853200-55862600	Weak transcription	Left Ventricle	heart
16	chr19:55853200-55862800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:55853200-55862800	Weak transcription	Primary B cells from cord blood	blood
18	chr19:55853200-55862800	Weak transcription	Osteobl	bone
19	chr19:55853400-55858000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:55853400-55859200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:55853400-55859600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr19:55853400-55859600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:55853400-55860000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:55853400-55860200	Strong transcription	Fetal Thymus	thymus
25	chr19:55853400-55860400	Strong transcription	Thymus	Thymus
26	chr19:55853400-55860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:55853400-55862200	Weak transcription	HepG2	liver
28	chr19:55853400-55864800	Weak transcription	Right Atrium	heart
29	chr19:55853600-55857600	Genic enhancers	Brain Germinal Matrix	brain
30	chr19:55853600-55858000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:55853600-55858600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:55853600-55859200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:55853600-55859200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:55853600-55861000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:55853600-55862400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:55853800-55857200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:55853800-55857200	Strong transcription	Right Ventricle	heart
38	chr19:55853800-55860600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:55854000-55860200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:55854400-55862200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:55854800-55857400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:55854800-55859200	Weak transcription	Fetal Lung	lung
43	chr19:55854800-55860000	Strong transcription	Fetal Brain Female	brain
44	chr19:55855000-55857400	Weak transcription	Pancreas	Pancrea
45	chr19:55855000-55859600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:55855200-55859600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:55855200-55860400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:55855200-55861800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:55855400-55857200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:55855400-55857400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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