Variant report

Variant	rs73546080
Chromosome Location	chr19:39847334-39847335
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	ELF1	chr19:39847188-39847557	K562	blood:	n/a	n/a
2	POLR2A	chr19:39847216-39847631	SK-N-MC	brain:	n/a	n/a
3	MAX	chr19:39847270-39847903	K562	blood:	n/a	n/a
4	USF1	chr19:39847289-39847713	K562	blood:	n/a	n/a
5	POLR2A	chr19:39847121-39847717	K562	blood:	n/a	n/a
6	MAX	chr19:39847241-39847579	K562	blood:	n/a	n/a
7	USF1	chr19:39847178-39847645	K562	blood:	n/a	n/a
8	IRF1	chr19:39846895-39847973	K562	blood:	n/a	chr19:39847336-39847350 chr19:39847229-39847239 chr19:39847281-39847288 chr19:39847225-39847239
9	E2F6	chr19:39847316-39847588	K562	blood:	n/a	n/a
10	MAZ	chr19:39847209-39847553	K562	blood:	n/a	n/a
11	CUX1	chr19:39847187-39847372	K562	blood:	n/a	n/a
12	MYC	chr19:39846761-39847935	K562	blood:	n/a	n/a
13	POLR2A	chr19:39847201-39847798	K562	blood:	n/a	n/a
14	HMGN3	chr19:39847134-39847550	K562	blood:	n/a	n/a
15	MAX	chr19:39847063-39847967	K562	blood:	n/a	n/a
16	SIN3AK20	chr19:39847211-39847566	K562	blood:	n/a	n/a
17	MXI1	chr19:39847226-39847748	K562	blood:	n/a	n/a
18	EP300	chr19:39846875-39847600	K562	blood:	n/a	n/a
19	POLR2A	chr19:39847295-39847834	K562	blood:	n/a	n/a
20	ZBTB7A	chr19:39847186-39847494	K562	blood:	n/a	n/a
21	MYC	chr19:39847213-39847800	K562	blood:	n/a	n/a
22	JUND	chr19:39847280-39847489	K562	blood:	n/a	n/a
23	RCOR1	chr19:39846756-39847523	K562	blood:	n/a	n/a
24	IRF1	chr19:39847207-39847549	K562	blood:	n/a	chr19:39847336-39847350 chr19:39847229-39847239 chr19:39847281-39847288 chr19:39847225-39847239
25	MYC	chr19:39846798-39847979	K562	blood:	n/a	n/a
26	CHD2	chr19:39847309-39847468	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39845453..39848424-chr19:39895764..39898971,3	K562	blood:
2	chr19:39843827..39847459-chr19:39858082..39862141,4	MCF-7	breast:
3	chr19:39846643..39848442-chr19:39897327..39899339,2	MCF-7	breast:
4	chr19:39845356..39848788-chr19:39900821..39905638,4	MCF-7	breast:

Variant related genes	Relation type
SAMD4B	TF binding region
ENSG00000090924	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs56222183	1.00[AMR][1000 genomes]
rs57536536	1.00[AMR][1000 genomes]
rs58949744	1.00[AMR][1000 genomes]
rs60577443	1.00[AMR][1000 genomes]
rs60840261	1.00[AMR][1000 genomes]
rs61112725	1.00[AMR][1000 genomes]
rs61124676	1.00[AMR][1000 genomes]
rs61213828	1.00[AMR][1000 genomes]
rs61595075	1.00[AMR][1000 genomes]
rs61730567	1.00[AMR][1000 genomes]
rs7250234	1.00[AMR][1000 genomes]
rs7250913	1.00[AMR][1000 genomes]
rs73544098	1.00[AMR][1000 genomes]
rs73546015	1.00[AMR][1000 genomes]
rs73546026	1.00[AMR][1000 genomes]
rs73547904	1.00[AMR][1000 genomes]
rs73547972	1.00[AMR][1000 genomes]
rs73553808	1.00[AMR][1000 genomes]
rs73553810	1.00[AMR][1000 genomes]
rs73553812	1.00[AMR][1000 genomes]
rs73553822	1.00[AMR][1000 genomes]
rs73553830	1.00[AMR][1000 genomes]
rs73553832	1.00[AMR][1000 genomes]
rs73553833	1.00[AMR][1000 genomes]
rs73553835	1.00[AMR][1000 genomes]
rs73553853	1.00[AMR][1000 genomes]
rs8101134	1.00[AMR][1000 genomes]

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	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic 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 miRNA target site	194 gene(s)	inside rSNPs	diseases
5	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	nsv520245	chr19:39844176-39850102	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv526707	chr19:39845544-39849955	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
11	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
4	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
8	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:39836000-39847600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
12	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
16	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
20	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
21	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:39838000-39851800	Strong transcription	Liver	Liver
23	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
24	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr19:39838400-39853200	Strong transcription	A549	lung
28	chr19:39838600-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:39839200-39851800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:39839200-39852600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:39839200-39853400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:39839200-39879200	Strong transcription	Dnd41	blood
37	chr19:39839800-39847400	Weak transcription	Fetal Heart	heart
38	chr19:39841000-39852600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:39841400-39852200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
41	chr19:39841800-39855400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:39842000-39851600	Strong transcription	HepG2	liver
43	chr19:39842000-39851800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr19:39842000-39852000	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr19:39842000-39864200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:39842400-39851400	Strong transcription	Fetal Brain Male	brain
50	chr19:39842400-39853200	Strong transcription	Rectal Mucosa Donor 31	rectum

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