Variant report

Variant	rs62335812
Chromosome Location	chr5:1884156-1884157
allele	A/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	SUZ12	chr5:1882701-1884720	NT2-D1	testis:	n/a	n/a
2	CTBP2	chr5:1882832-1885692	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:1882409-1891588	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:1882926-1884900	H1-neurons	neurons:	n/a	n/a
5	CTCF	chr5:1883806-1884301	MCF-7	breast:	n/a	chr5:1883982-1883995
6	POLR2A	chr5:1881878-1884205	MCF-7	breast:	n/a	n/a
7	MYC	chr5:1883027-1884765	MCF10A-Er-Src	breast:	n/a	chr5:1884034-1884044
8	CTCF	chr5:1883355-1884187	A549	lung:	n/a	chr5:1883982-1883995
9	MAX	chr5:1881264-1884334	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
10	HA-E2F1	chr5:1882707-1884473	MCF-7	breast:	n/a	chr5:1883113-1883122 chr5:1883355-1883367 chr5:1883515-1883525 chr5:1883115-1883124 chr5:1883975-1883985
11	MAX	chr5:1881356-1884611	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
12	SIN3A	chr5:1883880-1884158	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:1881893-1884225	MCF-7	breast:	n/a	n/a
14	CTCF	chr5:1883763-1884289	MCF-7	breast:	n/a	chr5:1883982-1883995
15	POLR2A	chr5:1884107-1884856	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
17	HDAC2	chr5:1883649-1884545	MCF-7	breast:	n/a	chr5:1884495-1884514
18	MAX	chr5:1881813-1884254	MCF-7	breast:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
19	RAD21	chr5:1883649-1884290	MCF-7	breast:	n/a	chr5:1883759-1883772
20	RAD21	chr5:1883692-1884166	H1-hESC	embryonic stem cell:	n/a	chr5:1883759-1883772
21	POLR2A	chr5:1881471-1884378	HCT-116	colon:	n/a	n/a
22	SUZ12	chr5:1884073-1884494	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr5:1883756-1884232	H1-hESC	embryonic stem cell:	n/a	chr5:1883759-1883772
24	TCF7L2	chr5:1882701-1884375	HCT-116	colon:	n/a	n/a
25	POLR2A	chr5:1883736-1884204	HCT-116	colon:	n/a	n/a
26	POLR2A	chr5:1883761-1884187	HCT-116	colon:	n/a	n/a

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:

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

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10062647	1.00[ASN][1000 genomes]
rs13162179	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232376	1.00[ASN][1000 genomes]
rs35249952	1.00[ASN][1000 genomes]
rs55664501	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335811	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335813	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:67 , 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	chr5:1881400-1884400	Bivalent Enhancer	Fetal Brain Male	brain
5	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach
6	chr5:1881600-1884200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:1881600-1884600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:1881600-1885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr5:1881800-1884200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:1882200-1884200	Enhancers	Primary hematopoietic stem cells	blood
11	chr5:1882200-1884600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr5:1882400-1884200	Bivalent Enhancer	Placenta	Placenta
13	chr5:1882400-1884600	Bivalent Enhancer	Lung	lung
14	chr5:1882400-1884800	Bivalent Enhancer	Spleen	Spleen
15	chr5:1882400-1885400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr5:1882400-1887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:1882400-1887600	Active TSS	NHEK	skin
18	chr5:1882400-1887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:1882600-1884200	Bivalent/Poised TSS	Psoas Muscle	Psoas
20	chr5:1882600-1884400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:1882600-1884400	Bivalent/Poised TSS	A549	lung
22	chr5:1882600-1884600	Active TSS	Left Ventricle	heart
23	chr5:1882600-1885000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:1882800-1884200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr5:1882800-1884200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr5:1882800-1884200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
27	chr5:1882800-1885000	Bivalent/Poised TSS	Esophagus	oesophagus
28	chr5:1883000-1884200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:1883000-1884400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr5:1883000-1884600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr5:1883000-1884600	Active TSS	Right Ventricle	heart
32	chr5:1883000-1884800	Active TSS	Fetal Heart	heart
33	chr5:1883000-1885200	Active TSS	HMEC	breast
34	chr5:1883200-1884400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
35	chr5:1883400-1884200	Enhancers	Pancreas	Pancrea
36	chr5:1883400-1884600	Bivalent Enhancer	Liver	Liver
37	chr5:1883600-1884200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr5:1883600-1884200	Enhancers	Gastric	stomach
39	chr5:1883600-1884200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
40	chr5:1883600-1884400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr5:1883600-1886800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:1883800-1884200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr5:1883800-1884200	Bivalent Enhancer	Adipose Nuclei	Adipose
44	chr5:1883800-1884200	Bivalent Enhancer	Ovary	ovary
45	chr5:1883800-1884200	Bivalent/Poised TSS	Right Atrium	heart
46	chr5:1883800-1884400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
47	chr5:1883800-1884400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
48	chr5:1883800-1884600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:1883800-1884600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
50	chr5:1883800-1884800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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