Variant report

Variant	rs563492309
Chromosome Location	chr5:1884532-1884533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:1884291-1884601	MCF10A-Er-Src	breast:	n/a	n/a
2	SUZ12	chr5:1882701-1884720	NT2-D1	testis:	n/a	n/a
3	CTBP2	chr5:1882832-1885692	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:1882409-1891588	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:1882926-1884900	H1-neurons	neurons:	n/a	n/a
6	FOS	chr5:1884338-1884711	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr5:1884358-1884637	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr5:1883027-1884765	MCF10A-Er-Src	breast:	n/a	chr5:1884034-1884044
9	MAX	chr5:1881356-1884611	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
10	STAT3	chr5:1884353-1884557	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr5:1884302-1884787	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr5:1884107-1884856	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr5:1884255-1884801	MCF10A-Er-Src	breast:	n/a	n/a
15	HDAC2	chr5:1883649-1884545	MCF-7	breast:	n/a	chr5:1884495-1884514
16	STAT3	chr5:1884348-1884553	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1884513-1884563	NHBE	bronchial:	n/a
2	chr5:1884513-1884563	HMEC	breast:	n/a
3	chr5:1884513-1884563	HepG2	liver:	n/a
4	chr5:1884513-1884563	H1-hESC	embryonic stem cell:	embryo
5	chr5:1884513-1884563	HCM	heart:	n/a
6	chr5:1884513-1884563	HRCEpiC	kidney:	n/a
7	chr5:1884513-1884563	Jurkat	blood:	n/a
8	chr5:1884513-1884563	AG09319	gingival:	n/a
9	chr5:1884513-1884563	GM12891	blood:	n/a
10	chr5:1884513-1884563	HEK293	kidney:	embryo
11	chr5:1884513-1884563	PrEC	prostate:	n/a
12	chr5:1884513-1884563	GM12892	blood:	n/a
13	chr5:1884513-1884563	ECC-1	luminal epithelium:	n/a
14	chr5:1884513-1884563	GM12878	blood:	n/a
15	chr5:1884513-1884563	SK-N-MC	brain:	n/a
16	chr5:1884513-1884563	SAEC	small airway:	n/a
17	chr5:1884513-1884563	HRE	kidney:	n/a
18	chr5:1884513-1884563	HPAEpiC	pulmonary alveolar:	n/a
19	chr5:1884513-1884563	GM06990	blood:	n/a
20	chr5:1884513-1884563	HIPEpiC	eye:	n/a
21	chr5:1884513-1884563	NB4	blood:	n/a
22	chr5:1884513-1884563	PFSK-1	brain:	n/a
23	chr5:1884513-1884563	MCF-7	breast:	n/a
24	chr5:1884513-1884563	HAEpiC	amniotic membrane:	n/a
25	chr5:1884513-1884563	AG04450	lung:	fetal
26	chr5:1884513-1884563	SKMC	muscle:	n/a
27	chr5:1884513-1884563	Hela-S3	cervix:	n/a
28	chr5:1884513-1884563	IMR90	lung:	fetal
29	chr5:1884513-1884563	A549	lung:	n/a
30	chr5:1884513-1884563	NT2-D1	testis:	n/a
31	chr5:1884513-1884563	AG10803	skin:	n/a
32	chr5:1884513-1884563	LNCaP	prostate:	n/a
33	chr5:1884513-1884563	T-47D	breast:	n/a
34	chr5:1884513-1884563	CMK	blood:	n/a
35	chr5:1884513-1884563	HCPEpiC	choroid plexus:	n/a
36	chr5:1884513-1884563	HL-60	blood:	n/a
37	chr5:1884513-1884563	PANC-1	pancreas:	n/a
38	chr5:1884513-1884563	ovcar-3	ovarian:	n/a
39	chr5:1884513-1884563	AG04449	skin:	fetal
40	chr5:1884513-1884563	AoSMC	blood vessel:	n/a
41	chr5:1884513-1884563	ProgFib	skin:	n/a
42	chr5:1884513-1884563	HCF	heart:	n/a
43	chr5:1884513-1884563	RPTEC	kidney:	n/a
44	chr5:1884513-1884563	NHDF-neo	bronchial:	n/a
45	chr5:1884513-1884563	HRPEpiC	eye:	n/a
46	chr5:1884513-1884563	AG09309	skin:	n/a
47	chr5:1884513-1884563	BE2_C	brain:	n/a
48	chr5:1884513-1884563	Caco-2	colon:	n/a
49	chr5:1884513-1884563	SK-N-SH	brain:	n/a
50	chr5:1884513-1884563	K562	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
2	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
3	chr5:1881475..1885354-chr5:1933918..1938503,4	MCF-7	breast:

No data

Variant related genes	Relation type
IRX4	TF binding region
ENSG00000249326	TF binding region
IRX4	CpG island
ENSG00000249326	CpG island
ENSG00000145494	Chromatin interaction
ENSG00000248994	Chromatin interaction
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	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
9	nsv1018082	chr5:1849721-1884738	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	nsv822963	chr5:1884480-1885198	Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1879800-1885200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr5:1880800-1887800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr5:1881200-1885200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach
5	chr5:1881600-1884600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:1881600-1885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr5:1882200-1884600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr5:1882400-1884600	Bivalent Enhancer	Lung	lung
9	chr5:1882400-1884800	Bivalent Enhancer	Spleen	Spleen
10	chr5:1882400-1885400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr5:1882400-1887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:1882400-1887600	Active TSS	NHEK	skin
13	chr5:1882400-1887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr5:1882600-1884600	Active TSS	Left Ventricle	heart
15	chr5:1882600-1885000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:1882800-1885000	Bivalent/Poised TSS	Esophagus	oesophagus
17	chr5:1883000-1884600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr5:1883000-1884600	Active TSS	Right Ventricle	heart
19	chr5:1883000-1884800	Active TSS	Fetal Heart	heart
20	chr5:1883000-1885200	Active TSS	HMEC	breast
21	chr5:1883400-1884600	Bivalent Enhancer	Liver	Liver
22	chr5:1883600-1886800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:1883800-1884600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:1883800-1884600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
25	chr5:1883800-1884800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:1883800-1885000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:1883800-1885400	Bivalent Enhancer	Brain Hippocampus Middle	brain
28	chr5:1884000-1884800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr5:1884000-1884800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:1884000-1884800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:1884000-1884800	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr5:1884000-1885000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:1884000-1885000	Bivalent Enhancer	Fetal Brain Female	brain
34	chr5:1884200-1884600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:1884200-1884600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr5:1884200-1884600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:1884200-1884600	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr5:1884200-1884800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr5:1884200-1884800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
40	chr5:1884200-1884800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
41	chr5:1884200-1884800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:1884200-1885400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr5:1884200-1885400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr5:1884200-1885600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:1884200-1898200	Weak transcription	Gastric	stomach
46	chr5:1884400-1884600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr5:1884400-1884600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:1884400-1884600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
49	chr5:1884400-1884600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:1884400-1884600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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