Variant report

Variant	rs55664501
Chromosome Location	chr5:1885206-1885207
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr5:1882832-1885692	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:1882409-1891588	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF143	chr5:1884757-1885262	H1-hESC	embryonic stem cell:	n/a	n/a
4	STAT3	chr5:1885079-1885337	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
6	SUZ12	chr5:1885091-1887033	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1885174-1885224	IMR90	lung:	fetal
2	chr5:1885174-1885224	GM19239	blood:	n/a
3	chr5:1885174-1885224	PrEC	prostate:	n/a
4	chr5:1885174-1885224	PFSK-1	brain:	n/a
5	chr5:1885174-1885224	HCF	heart:	n/a
6	chr5:1885174-1885224	HCM	heart:	n/a
7	chr5:1885174-1885224	HepG2	liver:	n/a
8	chr5:1885174-1885224	HCPEpiC	choroid plexus:	n/a
9	chr5:1885174-1885224	GM12892	blood:	n/a
10	chr5:1885174-1885224	AG09309	skin:	n/a
11	chr5:1885174-1885224	AG04450	lung:	fetal
12	chr5:1885174-1885224	NH-A	brain:	n/a
13	chr5:1885174-1885224	SKMC	muscle:	n/a
14	chr5:1885174-1885224	HIPEpiC	eye:	n/a
15	chr5:1885174-1885224	NB4	blood:	n/a
16	chr5:1885174-1885224	ECC-1	luminal epithelium:	n/a
17	chr5:1885174-1885224	A549	lung:	n/a
18	chr5:1885174-1885224	ovcar-3	ovarian:	n/a
19	chr5:1885174-1885224	AG04449	skin:	fetal
20	chr5:1885174-1885224	HRE	kidney:	n/a
21	chr5:1885174-1885224	HPAEpiC	pulmonary alveolar:	n/a
22	chr5:1885174-1885224	HCT-116	colon:	n/a
23	chr5:1885174-1885224	SAEC	small airway:	n/a
24	chr5:1885174-1885224	SK-N-SH	brain:	n/a
25	chr5:1885174-1885224	NHBE	bronchial:	n/a
26	chr5:1885174-1885224	RPTEC	kidney:	n/a
27	chr5:1885174-1885224	MCF-7	breast:	n/a
28	chr5:1885174-1885224	HUVEC	blood vessel:	n/a
29	chr5:1885174-1885224	HEEpiC	esophagus:	n/a
30	chr5:1885174-1885224	T-47D	breast:	n/a
31	chr5:1885174-1885224	HNPCEpiC	eye:	n/a
32	chr5:1885174-1885224	HL-60	blood:	n/a
33	chr5:1885174-1885224	H1-hESC	embryonic stem cell:	embryo
34	chr5:1885174-1885224	HEK293	kidney:	embryo
35	chr5:1885174-1885224	Hela-S3	cervix:	n/a
36	chr5:1885174-1885224	ProgFib	skin:	n/a
37	chr5:1885174-1885224	LNCaP	prostate:	n/a
38	chr5:1885174-1885224	BE2_C	brain:	n/a
39	chr5:1885174-1885224	GM12878	blood:	n/a
40	chr5:1885174-1885224	Caco-2	colon:	n/a
41	chr5:1885174-1885224	HRCEpiC	kidney:	n/a
42	chr5:1885174-1885224	CMK	blood:	n/a
43	chr5:1885174-1885224	HRPEpiC	eye:	n/a
44	chr5:1885174-1885224	AG10803	skin:	n/a
45	chr5:1885174-1885224	HMEC	breast:	n/a
46	chr5:1885174-1885224	SK-N-SH_RA	brain:	n/a
47	chr5:1885174-1885224	BJ	skin:	n/a
48	chr5:1885174-1885224	Hepatocyte	liver:	n/a
49	chr5:1885174-1885224	AG09319	gingival:	n/a
50	chr5:1885174-1885224	SK-N-MC	brain:	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
ENSG00000249326	TF binding region
IRX4	TF binding region
ENSG00000249326	CpG island
IRX4	CpG island
ENSG00000248994	Chromatin interaction
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10062647	0.90[ASN][1000 genomes]
rs13162179	0.87[EUR][1000 genomes]
rs2232376	0.90[ASN][1000 genomes]
rs34414799	0.89[ASN][1000 genomes]
rs35249952	0.90[ASN][1000 genomes]
rs62335811	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62335812	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335813	0.90[ASN][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	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	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:41 , 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	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach
3	chr5:1881600-1885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr5:1882400-1885400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr5:1882400-1887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:1882400-1887600	Active TSS	NHEK	skin
7	chr5:1882400-1887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr5:1883600-1886800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:1883800-1885400	Bivalent Enhancer	Brain Hippocampus Middle	brain
10	chr5:1884200-1885400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr5:1884200-1885400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
12	chr5:1884200-1885600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:1884200-1898200	Weak transcription	Gastric	stomach
14	chr5:1884400-1886000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:1884400-1886400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:1884400-1887000	Weak transcription	Right Atrium	heart
17	chr5:1884800-1885400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr5:1884800-1885400	Bivalent Enhancer	Lung	lung
19	chr5:1884800-1885600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr5:1884800-1886400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr5:1885000-1885400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:1885000-1885400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:1885000-1885400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr5:1885000-1885400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:1885000-1885400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:1885000-1885400	Enhancers	Right Ventricle	heart
27	chr5:1885000-1885600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:1885000-1886600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:1885000-1887800	Active TSS	Esophagus	oesophagus
30	chr5:1885200-1885400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr5:1885200-1885400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
32	chr5:1885200-1885400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr5:1885200-1885400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr5:1885200-1885400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:1885200-1885400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:1885200-1885400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
37	chr5:1885200-1885400	Transcr. at gene 5' and 3'	HMEC	breast
38	chr5:1885200-1885600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr5:1885200-1885600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:1885200-1885800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:1885200-1886600	Active TSS	Fetal Heart	heart

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