Variant report

Variant	rs549874604
Chromosome Location	chr5:1887004-1887005
allele	-/GT
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1882409-1891588	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr5:1886970-1887632	MCF10A-Er-Src	breast:	n/a	chr5:1887356-1887365
3	CTBP2	chr5:1885936-1887086	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
5	SUZ12	chr5:1885091-1887033	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1886994-1887044	HCT-116	colon:	n/a
2	chr5:1886956-1887006	HRE	kidney:	n/a
3	chr5:1886994-1887044	Jurkat	blood:	n/a
4	chr5:1886956-1887006	U87	brain:	n/a
5	chr5:1886994-1887044	SK-N-SH	brain:	n/a
6	chr5:1886956-1887006	SKMC	muscle:	n/a
7	chr5:1886956-1887006	ECC-1	luminal epithelium:	n/a
8	chr5:1886994-1887044	SK-N-SH_RA	brain:	n/a
9	chr5:1886956-1887006	AoSMC	blood vessel:	n/a
10	chr5:1886956-1887006	NHBE	bronchial:	n/a
11	chr5:1886994-1887044	CMK	blood:	n/a
12	chr5:1886994-1887044	NHDF-neo	bronchial:	n/a
13	chr5:1886956-1887006	AG10803	skin:	n/a
14	chr5:1886994-1887044	HEEpiC	esophagus:	n/a
15	chr5:1886956-1887006	SAEC	small airway:	n/a
16	chr5:1886956-1887006	MCF10A-Er-Src	breast:	n/a
17	chr5:1886994-1887044	AG09309	skin:	n/a
18	chr5:1886956-1887006	CMK	blood:	n/a
19	chr5:1886956-1887006	GM12878	blood:	n/a
20	chr5:1886956-1887006	PrEC	prostate:	n/a
21	chr5:1886956-1887006	GM19239	blood:	n/a
22	chr5:1886994-1887044	A549	lung:	n/a
23	chr5:1886994-1887044	Caco-2	colon:	n/a
24	chr5:1886956-1887006	MCF-7	breast:	n/a
25	chr5:1886956-1887006	NHDF-neo	bronchial:	n/a
26	chr5:1886994-1887044	HCM	heart:	n/a
27	chr5:1886956-1887006	ovcar-3	ovarian:	n/a
28	chr5:1886994-1887044	SAEC	small airway:	n/a
29	chr5:1886956-1887006	HRPEpiC	eye:	n/a
30	chr5:1886956-1887006	HAEpiC	amniotic membrane:	n/a
31	chr5:1886956-1887006	HRCEpiC	kidney:	n/a
32	chr5:1886994-1887044	GM06990	blood:	n/a
33	chr5:1886956-1887006	AG04450	lung:	fetal
34	chr5:1886994-1887044	HRCEpiC	kidney:	n/a
35	chr5:1886956-1887006	HEEpiC	esophagus:	n/a
36	chr5:1886994-1887044	GM12892	blood:	n/a
37	chr5:1886994-1887044	HIPEpiC	eye:	n/a
38	chr5:1886994-1887044	HEK293	kidney:	embryo
39	chr5:1886956-1887006	Hela-S3	cervix:	n/a
40	chr5:1886956-1887006	GM06990	blood:	n/a
41	chr5:1886994-1887044	BJ	skin:	n/a
42	chr5:1886956-1887006	SK-N-SH	brain:	n/a
43	chr5:1886956-1887006	HL-60	blood:	n/a
44	chr5:1886994-1887044	NH-A	brain:	n/a
45	chr5:1886956-1887006	Caco-2	colon:	n/a
46	chr5:1886956-1887006	GM12891	blood:	n/a
47	chr5:1886956-1887006	AG09309	skin:	n/a
48	chr5:1886956-1887006	SK-N-MC	brain:	n/a
49	chr5:1886994-1887044	HRE	kidney:	n/a
50	chr5:1886994-1887044	AG09319	gingival:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1669626..1671226-chr5:1885591..1887218,2	MCF-7	breast:
2	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
3	chr5:1799569..1802884-chr5:1886598..1889173,4	MCF-7	breast:

No data

Variant related genes	Relation type
IRX4	TF binding region
ENSG00000249326	TF binding region
ENSG00000249326	CpG island
IRX4	CpG island
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv596893	chr5:1839498-1892759	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv881470	chr5:1850563-1892759	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881188	chr5:1852284-1892759	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv822962	chr5:1877770-1888630	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv880886	chr5:1880891-1936443	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	esv3407995	chr5:1885777-1888525	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv880460	chr5:1886471-1936443	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1880800-1887800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr5:1882400-1887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:1882400-1887600	Active TSS	NHEK	skin
4	chr5:1882400-1887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr5:1884200-1898200	Weak transcription	Gastric	stomach
6	chr5:1885000-1887800	Active TSS	Esophagus	oesophagus
7	chr5:1885400-1887400	Active TSS	HMEC	breast
8	chr5:1885400-1887600	Active TSS	Right Ventricle	heart
9	chr5:1885400-1887800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:1885600-1887800	Active TSS	Left Ventricle	heart
11	chr5:1886000-1887600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:1886000-1888200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr5:1886200-1887600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr5:1886200-1887800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr5:1886200-1888000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:1886200-1888000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr5:1886400-1887400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:1886400-1887600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:1886400-1887800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr5:1886400-1888000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:1886600-1887400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr5:1886600-1887600	Bivalent Enhancer	Fetal Brain Male	brain
23	chr5:1886600-1887600	Weak transcription	Fetal Heart	heart
24	chr5:1886600-1887800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:1886600-1887800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:1886600-1887800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr5:1886800-1887400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:1886800-1887400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:1886800-1887400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
30	chr5:1886800-1887400	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr5:1886800-1887400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr5:1886800-1887600	Enhancers	Liver	Liver
33	chr5:1886800-1887800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:1886800-1887800	Bivalent Enhancer	Brain Germinal Matrix	brain
35	chr5:1887000-1887200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:1887000-1887400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:1887000-1887400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:1887000-1887400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:1887000-1887600	Bivalent/Poised TSS	Psoas Muscle	Psoas
40	chr5:1887000-1887600	Active TSS	Right Atrium	heart
41	chr5:1887000-1887800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr5:1887000-1888000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links