Variant report

Variant	rs553948247
Chromosome Location	chr19:18496532-18496533
allele	C/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	MYC	chr19:18496101-18496664	MCF10A-Er-Src	breast:	n/a	n/a
2	RCOR1	chr19:18496131-18498156	IMR90	lung:	n/a	n/a
3	FOS	chr19:18496205-18496602	MCF10A-Er-Src	breast:	n/a	n/a
4	MAZ	chr19:18496304-18498087	IMR90	lung:	n/a	chr19:18496883-18496893
5	MYC	chr19:18496411-18497925	K562	blood:	n/a	chr19:18496883-18496893
6	MYBL2	chr19:18496306-18497377	HepG2	liver:	n/a	n/a
7	GTF2F1	chr19:18496423-18498128	Hela-S3	cervix:	n/a	n/a
8	MAFK	chr19:18496454-18497205	HepG2	liver:	n/a	n/a
9	FOXA1	chr19:18496532-18497107	HepG2	liver:	n/a	n/a
10	HEY1	chr19:18496398-18497219	HepG2	liver:	n/a	n/a
11	SP1	chr19:18496300-18497219	HepG2	liver:	n/a	chr19:18496847-18496856 chr19:18496845-18496857 chr19:18496845-18496857 chr19:18496885-18496899 chr19:18496846-18496855 chr19:18496895-18496907 chr19:18496846-18496855 chr19:18496892-18496906
12	HNF4G	chr19:18496391-18497248	HepG2	liver:	n/a	chr19:18496607-18496620 chr19:18496605-18496620 chr19:18496920-18496934 chr19:18496920-18496935 chr19:18496607-18496619 chr19:18496604-18496622 chr19:18496606-18496620 chr19:18496607-18496619 chr19:18496606-18496619 chr19:18496606-18496620 chr19:18496605-18496620 chr19:18496920-18496935 chr19:18496613-18496620
13	TCF12	chr19:18496528-18497260	ECC-1	luminal epithelium:	n/a	n/a
14	JUND	chr19:18496391-18497300	HepG2	liver:	n/a	n/a
15	NFIC	chr19:18496276-18497257	HepG2	liver:	n/a	n/a
16	GATA2	chr19:18496185-18497519	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:18496339-18498714	HUVEC	blood vessel:	n/a	n/a
18	EP300	chr19:18496278-18498015	K562	blood:	n/a	chr19:18497691-18497705 chr19:18496533-18496540 chr19:18496872-18496882
19	FOSL2	chr19:18496325-18497309	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:18496202-18502123	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr19:18496258-18501948	HCT-116	colon:	n/a	n/a
22	MXI1	chr19:18496364-18497225	HepG2	liver:	n/a	n/a
23	MAX	chr19:18496288-18498036	A549	lung:	n/a	chr19:18496883-18496893
24	MAFF	chr19:18496431-18497156	HepG2	liver:	n/a	n/a
25	HDAC2	chr19:18496438-18497266	HepG2	liver:	n/a	chr19:18496628-18496642 chr19:18496872-18496881
26	EBF1	chr19:18496528-18496677	GM12878	blood:	n/a	n/a
27	SP1	chr19:18496383-18497312	A549	lung:	n/a	chr19:18496847-18496856 chr19:18496845-18496857 chr19:18496845-18496857 chr19:18496885-18496899 chr19:18496846-18496855 chr19:18496895-18496907 chr19:18496846-18496855 chr19:18496892-18496906
28	JUN	chr19:18496099-18498685	K562	blood:	n/a	chr19:18498525-18498534 chr19:18497901-18497912
29	REST	chr19:18496521-18497840	A549	lung:	n/a	chr19:18496886-18496899
30	FOS	chr19:18496203-18497160	HUVEC	blood vessel:	n/a	n/a
31	MAZ	chr19:18496377-18497253	HepG2	liver:	n/a	chr19:18496883-18496893
32	JUN	chr19:18496437-18496998	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:18495086-18501822	HepG2	liver:	n/a	n/a
34	MYBL2	chr19:18496124-18498233	HepG2	liver:	n/a	n/a
35	POLR2A	chr19:18495056-18501851	HepG2	liver:	n/a	n/a
36	HNF4A	chr19:18496387-18497294	HepG2	liver:	n/a	chr19:18496607-18496620 chr19:18496605-18496620 chr19:18496920-18496934 chr19:18496920-18496935 chr19:18496607-18496619 chr19:18496604-18496622 chr19:18496606-18496620 chr19:18496607-18496619 chr19:18496919-18496934 chr19:18496606-18496619 chr19:18496606-18496620 chr19:18496605-18496620 chr19:18496920-18496935 chr19:18496613-18496620
37	POLR2A	chr19:18496402-18498400	HepG2	liver:	n/a	n/a
38	MAFK	chr19:18496310-18497240	K562	blood:	n/a	n/a
39	POLR2A	chr19:18496418-18496590	HepG2	liver:	n/a	n/a
40	ELF1	chr19:18496379-18497185	HepG2	liver:	n/a	n/a
41	MYC	chr19:18496420-18496720	HUVEC	blood vessel:	n/a	n/a
42	TCF12	chr19:18496250-18498287	A549	lung:	n/a	chr19:18497672-18497679
43	RCOR1	chr19:18496363-18497283	K562	blood:	n/a	n/a
44	MBD4	chr19:18496419-18497317	HepG2	liver:	n/a	n/a
45	MAX	chr19:18496431-18497233	HepG2	liver:	n/a	chr19:18496883-18496893
46	NR2F2	chr19:18496372-18497266	K562	blood:	n/a	n/a
47	KAP1	chr19:18496183-18497221	U2OS	brain:	n/a	n/a
48	HNF4A	chr19:18496455-18497170	HepG2	liver:	n/a	chr19:18496607-18496620 chr19:18496605-18496620 chr19:18496920-18496934 chr19:18496920-18496935 chr19:18496607-18496619 chr19:18496604-18496622 chr19:18496606-18496620 chr19:18496607-18496619 chr19:18496919-18496934 chr19:18496606-18496619 chr19:18496606-18496620 chr19:18496605-18496620 chr19:18496920-18496935 chr19:18496613-18496620
49	TEAD4	chr19:18496121-18498431	K562	blood:	n/a	chr19:18498034-18498043
50	MAZ	chr19:18496253-18498019	K562	blood:	n/a	chr19:18496883-18496893

No.	Distal block	Cell Line	Cell type
1	chr19:18495232..18499014-chr19:18539147..18542857,5	K562	blood:
2	chr19:18493661..18496655-chr19:45595897..45597590,2	MCF-7	breast:
3	chr19:18207159..18210021-chr19:18495217..18497699,3	K562	blood:
4	chr19:18496334..18499990-chr19:18526862..18529675,5	MCF-7	breast:
5	chr19:18466669..18468716-chr19:18495556..18498014,2	MCF-7	breast:
6	chr19:18495663..18499199-chr19:18698556..18701601,3	K562	blood:
7	chr19:18495538..18497928-chr19:18546871..18549099,2	MCF-7	breast:
8	chr19:18495466..18501669-chr19:18543275..18549976,8	K562	blood:
9	chr19:18495925..18498880-chr19:18550697..18553844,3	K562	blood:
10	chr19:18334018..18336391-chr19:18495614..18498582,2	K562	blood:
11	chr19:18495115..18497091-chr19:18555323..18558164,2	MCF-7	breast:
12	chr19:18495627..18501937-chr19:18519170..18524838,12	K562	blood:
13	chr19:18387676..18394124-chr19:18495437..18503905,30	K562	blood:
14	chr19:18494076..18504244-chr19:18508099..18514509,16	MCF-7	breast:
15	chr19:18207432..18210021-chr19:18495854..18497699,2	K562	blood:
16	chr19:18387676..18394344-chr19:18495021..18501696,25	K562	blood:
17	chr19:18443925..18446032-chr19:18496432..18498397,2	MCF-7	breast:
18	chr19:18448228..18453626-chr19:18495351..18501647,22	K562	blood:
19	chr12:66563193..66563791-chr19:18496498..18497271,2	HCT-116	colon:
20	chr19:18495971..18498335-chr19:18520063..18523312,3	MCF-7	breast:
21	chr19:18495547..18503463-chr19:18525062..18531964,43	K562	blood:
22	chr19:18366000..18368081-chr19:18496132..18498337,2	K562	blood:

Variant related genes	Relation type
GDF15	TF binding region
MIR3189	TF binding region
ENSG00000096996	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000268199	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000175489	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS 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	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv2430	chr19:18496428-18514937	Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18485800-18496600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr19:18485800-18499000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18486400-18496600	Weak transcription	Fetal Kidney	kidney
4	chr19:18488600-18496800	Enhancers	Placenta	Placenta
5	chr19:18491400-18497400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:18491600-18497400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:18491800-18496600	Weak transcription	Osteobl	bone
8	chr19:18491800-18496800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:18491800-18496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:18491800-18496800	Weak transcription	Colonic Mucosa	Colon
11	chr19:18491800-18496800	Weak transcription	Right Atrium	heart
12	chr19:18491800-18497000	Weak transcription	Lung	lung
13	chr19:18492000-18498800	Weak transcription	Right Ventricle	heart
14	chr19:18493800-18497600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:18494200-18496600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:18494200-18496600	Weak transcription	HSMM	muscle
17	chr19:18495000-18496800	Enhancers	Fetal Intestine Small	intestine
18	chr19:18495200-18496600	Flanking Active TSS	HepG2	liver
19	chr19:18495200-18496800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:18495200-18497000	Enhancers	Fetal Intestine Large	intestine
21	chr19:18495400-18496600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr19:18495600-18497000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:18495600-18497200	Enhancers	Stomach Mucosa	stomach
24	chr19:18495800-18496800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:18495800-18497000	Enhancers	Liver	Liver
26	chr19:18495800-18497200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:18495800-18497400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr19:18496000-18496800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:18496000-18496800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:18496000-18496800	Enhancers	Pancreas	Pancrea
31	chr19:18496000-18496800	Enhancers	HMEC	breast
32	chr19:18496200-18496600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:18496200-18496600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr19:18496200-18496800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:18496200-18496800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:18496200-18496800	Enhancers	Gastric	stomach
37	chr19:18496200-18496800	Enhancers	Small Intestine	intestine
38	chr19:18496200-18496800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
39	chr19:18496200-18496800	Flanking Active TSS	A549	lung
40	chr19:18496200-18496800	Flanking Active TSS	Hela-S3	cervix
41	chr19:18496200-18497000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:18496200-18497000	Enhancers	GM12878-XiMat	blood
43	chr19:18496200-18497200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:18496200-18497400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr19:18496400-18496600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr19:18496400-18496600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:18496400-18496600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr19:18496400-18496600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:18496400-18496600	Enhancers	HSMMtube	muscle
50	chr19:18496400-18496600	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links