Variant report

Variant	rs554834387
Chromosome Location	chr19:19009827-19009828
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	GATA1	chr19:19008888-19009932	K562	blood:	n/a	chr19:19009565-19009582 chr19:19009574-19009583 chr19:19009558-19009565 chr19:19009558-19009567 chr19:19009558-19009565 chr19:19009558-19009565 chr19:19009576-19009586
2	POLR2A	chr19:19009067-19010565	K562	blood:	n/a	n/a
3	NR2F2	chr19:19009311-19009949	MCF-7	breast:	n/a	chr19:19009593-19009608
4	CEBPD	chr19:19009297-19009827	K562	blood:	n/a	n/a
5	POLR2A	chr19:19009782-19009827	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:19009317-19009858	SK-N-SH	brain:	n/a	n/a
7	CEBPD	chr19:19009301-19009848	K562	blood:	n/a	n/a
8	NR2F2	chr19:19009150-19009843	K562	blood:	n/a	chr19:19009593-19009608
9	POLR2A	chr19:19008845-19010363	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:19009371-19010069	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:19009379-19010358	GM12892	blood:	n/a	n/a
12	MTA3	chr19:19009070-19010062	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19008885-19010322	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:19008890-19010280	K562	blood:	n/a	n/a
15	POLR2A	chr19:19009704-19010279	K562	blood:	n/a	n/a
16	POLR2A	chr19:19008817-19010156	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr19:19009244-19011075	GM12891	blood:	n/a	n/a
18	HMGN3	chr19:19008984-19009957	K562	blood:	n/a	n/a
19	POLR2A	chr19:19009278-19009888	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:19009315-19010290	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr19:19009779-19009932	A549	lung:	n/a	n/a
22	POLR2A	chr19:19008937-19010250	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:19009569-19010002	HCT-116	colon:	n/a	n/a
24	POLR2A	chr19:19008964-19011058	K562	blood:	n/a	n/a
25	POLR2A	chr19:19009293-19010260	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr19:19009289-19010337	A549	lung:	n/a	n/a
27	POLR2A	chr19:19008935-19012494	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:19009400-19010124	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr19:19008989-19010421	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:19009279-19010374	HL-60	blood:	n/a	n/a
31	POLR2A	chr19:19008894-19010240	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:19009327-19010103	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:19009304-19010335	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:19008886-19010266	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:19009283-19010188	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:19008955-19010345	HL-60	blood:	n/a	n/a
37	POLR2A	chr19:19009340-19010357	GM12891	blood:	n/a	n/a
38	POLR2A	chr19:19009184-19010337	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:19008966-19010219	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:19008876-19012538	K562	blood:	n/a	n/a
41	BRCA1	chr19:19009826-19009852	HepG2	liver:	n/a	n/a
42	POLR2A	chr19:19008808-19009923	U87	brain:	n/a	n/a
43	POLR2A	chr19:19009473-19009840	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:19009461-19010053	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19008851..19010420-chr19:19035551..19037561,2	K562	blood:
2	chr19:19008286..19009845-chr19:19027692..19029739,2	MCF-7	breast:
3	chr19:18993425..18995899-chr19:19009767..19011976,2	K562	blood:
4	chr19:19009093..19010811-chr19:19050023..19052149,2	MCF-7	breast:

Variant related genes	Relation type
GDF1	TF binding region
CERS1	TF binding region
ENSG00000269019	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000223802	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh 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	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	esv1823390	chr19:19006569-19017777	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv817819	chr19:19009470-19022204	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19006400-19011000	Weak transcription	Fetal Lung	lung
2	chr19:19006600-19010000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:19006600-19010000	Weak transcription	Gastric	stomach
4	chr19:19006600-19016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:19006600-19027800	Weak transcription	NHDF-Ad	bronchial
6	chr19:19006600-19029000	Weak transcription	Fetal Kidney	kidney
7	chr19:19006800-19010000	Weak transcription	Left Ventricle	heart
8	chr19:19006800-19011200	Weak transcription	Primary B cells from cord blood	blood
9	chr19:19006800-19017800	Weak transcription	HUVEC	blood vessel
10	chr19:19007000-19010000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19007000-19010000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:19007000-19029000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:19007400-19025400	Weak transcription	NH-A	brain
14	chr19:19007400-19026000	Weak transcription	A549	lung
15	chr19:19007400-19027800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:19007600-19010000	Weak transcription	Pancreas	Pancrea
17	chr19:19007600-19010400	Weak transcription	Ovary	ovary
18	chr19:19007600-19010800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:19007600-19015400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:19007600-19017000	Weak transcription	Brain Angular Gyrus	brain
21	chr19:19007600-19018200	Weak transcription	HSMM	muscle
22	chr19:19007600-19018600	Weak transcription	HMEC	breast
23	chr19:19007600-19028600	Weak transcription	Right Atrium	heart
24	chr19:19007800-19010200	Weak transcription	Brain Substantia Nigra	brain
25	chr19:19007800-19010200	Weak transcription	Osteobl	bone
26	chr19:19008000-19010000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:19008000-19010000	Enhancers	Fetal Intestine Large	intestine
28	chr19:19008000-19010200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:19008000-19010600	Weak transcription	Brain Anterior Caudate	brain
30	chr19:19008000-19012400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:19008200-19016000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:19008200-19026000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:19008400-19010000	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:19008400-19010200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:19008400-19011600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:19008400-19012000	Strong transcription	Fetal Stomach	stomach
37	chr19:19008400-19014000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:19008400-19014400	Weak transcription	NHEK	skin
39	chr19:19008400-19017400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:19008400-19018600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:19008600-19010000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:19008600-19010000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:19008600-19012200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:19008600-19014000	Weak transcription	Small Intestine	intestine
45	chr19:19008600-19015200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:19008800-19010200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:19008800-19010200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:19008800-19024200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19009000-19010000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:19009200-19010000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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