Variant report

Variant	rs6876836
Chromosome Location	chr5:1882900-1882901
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	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	TBP	chr5:1882716-1883054	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr5:1882819-1883840	A549	lung:	n/a	n/a
5	POLR2A	chr5:1882409-1891588	MCF10A-Er-Src	breast:	n/a	n/a
6	CREB1	chr5:1882873-1883389	H1-hESC	embryonic stem cell:	n/a	chr5:1883112-1883125
7	MAX	chr5:1881127-1883194	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
8	YY1	chr5:1882638-1882941	H1-hESC	embryonic stem cell:	n/a	chr5:1882641-1882652 chr5:1882813-1882824
9	MAX	chr5:1881155-1883265	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
10	POLR2A	chr5:1881878-1884205	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:1881879-1883664	HCT-116	colon:	n/a	n/a
12	E2F6	chr5:1881274-1883118	H1-hESC	embryonic stem cell:	n/a	chr5:1882416-1882427 chr5:1882410-1882425 chr5:1881643-1881650 chr5:1881643-1881650 chr5:1882417-1882427 chr5:1882415-1882426 chr5:1881643-1881650 chr5:1882245-1882254 chr5:1882411-1882425
13	MAX	chr5:1881264-1884334	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
14	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
15	POLR2A	chr5:1882270-1883236	ProgFib	skin:	n/a	n/a
16	MAX	chr5:1881356-1884611	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
17	HDAC2	chr5:1882149-1883364	MCF-7	breast:	n/a	chr5:1883042-1883056 chr5:1883039-1883053 chr5:1883045-1883059 chr5:1883044-1883058 chr5:1883040-1883054 chr5:1883043-1883057
18	POLR2A	chr5:1882557-1884114	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:1881359-1883606	HCT-116	colon:	n/a	n/a
20	POLR2A	chr5:1881893-1884225	MCF-7	breast:	n/a	n/a
21	MAZ	chr5:1882842-1883448	IMR90	lung:	n/a	n/a
22	YY1	chr5:1882586-1883004	H1-hESC	embryonic stem cell:	n/a	chr5:1882641-1882652 chr5:1882813-1882824
23	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
24	YY1	chr5:1882645-1882900	HCT-116	colon:	n/a	chr5:1882813-1882824
25	MAX	chr5:1881813-1884254	MCF-7	breast:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
26	CHD2	chr5:1882880-1882969	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr5:1881471-1884378	HCT-116	colon:	n/a	n/a
28	SIN3A	chr5:1882507-1883051	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF7L2	chr5:1882701-1884375	HCT-116	colon:	n/a	n/a
30	E2F6	chr5:1882818-1883236	A549	lung:	n/a	chr5:1883113-1883122 chr5:1883115-1883124

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1882871-1882921	GM12878	blood:	n/a
2	chr5:1882885-1882935	Caco-2	colon:	n/a
3	chr5:1882871-1882921	HRE	kidney:	n/a
4	chr5:1882871-1882921	NT2-D1	testis:	n/a
5	chr5:1882900-1882950	A549	lung:	n/a
6	chr5:1882900-1882950	Hepatocyte	liver:	n/a
7	chr5:1882871-1882921	LNCaP	prostate:	n/a
8	chr5:1882885-1882935	CMK	blood:	n/a
9	chr5:1882871-1882921	HCF	heart:	n/a
10	chr5:1882871-1882921	HL-60	blood:	n/a
11	chr5:1882900-1882950	HNPCEpiC	eye:	n/a
12	chr5:1882885-1882935	MCF-7	breast:	n/a
13	chr5:1882885-1882935	NHDF-neo	bronchial:	n/a
14	chr5:1882900-1882950	NB4	blood:	n/a
15	chr5:1882871-1882921	AoSMC	blood vessel:	n/a
16	chr5:1882885-1882935	PrEC	prostate:	n/a
17	chr5:1882885-1882935	PFSK-1	brain:	n/a
18	chr5:1882885-1882935	NB4	blood:	n/a
19	chr5:1882900-1882950	H1-hESC	embryonic stem cell:	embryo
20	chr5:1882885-1882935	AG04450	lung:	fetal
21	chr5:1882871-1882921	K562	blood:	n/a
22	chr5:1882885-1882935	HRPEpiC	eye:	n/a
23	chr5:1882900-1882950	HCPEpiC	choroid plexus:	n/a
24	chr5:1882900-1882950	HL-60	blood:	n/a
25	chr5:1882900-1882950	HCM	heart:	n/a
26	chr5:1882871-1882921	SK-N-SH	brain:	n/a
27	chr5:1882900-1882950	HRE	kidney:	n/a
28	chr5:1882871-1882921	BJ	skin:	n/a
29	chr5:1882885-1882935	AG10803	skin:	n/a
30	chr5:1882885-1882935	SK-N-SH_RA	brain:	n/a
31	chr5:1882871-1882921	HEK293	kidney:	embryo
32	chr5:1882871-1882921	SK-N-SH_RA	brain:	n/a
33	chr5:1882900-1882950	Hela-S3	cervix:	n/a
34	chr5:1882871-1882921	IMR90	lung:	fetal
35	chr5:1882871-1882921	HUVEC	blood vessel:	n/a
36	chr5:1882900-1882950	PrEC	prostate:	n/a
37	chr5:1882885-1882935	ovcar-3	ovarian:	n/a
38	chr5:1882885-1882935	HepG2	liver:	n/a
39	chr5:1882900-1882950	HCF	heart:	n/a
40	chr5:1882885-1882935	ECC-1	luminal epithelium:	n/a
41	chr5:1882871-1882921	MCF10A-Er-Src	breast:	n/a
42	chr5:1882871-1882921	Caco-2	colon:	n/a
43	chr5:1882885-1882935	HCPEpiC	choroid plexus:	n/a
44	chr5:1882900-1882950	HepG2	liver:	n/a
45	chr5:1882885-1882935	GM12892	blood:	n/a
46	chr5:1882871-1882921	RPTEC	kidney:	n/a
47	chr5:1882871-1882921	Hepatocyte	liver:	n/a
48	chr5:1882885-1882935	SAEC	small airway:	n/a
49	chr5:1882900-1882950	AG04449	skin:	fetal
50	chr5:1882885-1882935	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
2	chr5:1799841..1802509-chr5:1881368..1882987,2	K562	blood:
3	chr17:57923026..57925305-chr5:1880876..1883150,2	MCF-7	breast:
4	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
5	chr21:43186959..43187774-chr5:1882557..1883522,2	HCT-116	colon:
6	chr5:1881475..1885354-chr5:1933918..1938503,4	MCF-7	breast:
7	chr5:1798942..1801341-chr5:1879541..1882987,3	K562	blood:

Variant related genes	Relation type
IRX4	TF binding region
ENSG00000249326	TF binding region
ENSG00000249116	TF binding region
IRX4	CpG island
ENSG00000249326	CpG island
ENSG00000249116	CpG island
ENSG00000183421	Chromatin interaction
ENSG00000145494	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000171421	Chromatin interaction
ENSG00000248994	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10474731	0.82[ASN][1000 genomes]
rs1632597	0.86[ASN][1000 genomes]
rs1689718	0.97[ASN][1000 genomes]
rs260402	0.99[ASN][1000 genomes]

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	esv16732	chr5:1880874-1883019	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1878600-1883000	Enhancers	Fetal Heart	heart
2	chr5:1879800-1885200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:1880800-1887800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr5:1881200-1885200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:1881400-1884400	Bivalent Enhancer	Fetal Brain Male	brain
6	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach
7	chr5:1881600-1883000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:1881600-1883200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:1881600-1883200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:1881600-1883200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:1881600-1883800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:1881600-1884200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:1881600-1884600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:1881600-1885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr5:1881800-1883000	Bivalent Enhancer	Colonic Mucosa	Colon
16	chr5:1881800-1883000	Flanking Active TSS	Right Ventricle	heart
17	chr5:1881800-1883600	Weak transcription	Gastric	stomach
18	chr5:1881800-1884200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:1882000-1883000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr5:1882200-1883000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
21	chr5:1882200-1884200	Enhancers	Primary hematopoietic stem cells	blood
22	chr5:1882200-1884600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr5:1882400-1883000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr5:1882400-1883200	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr5:1882400-1883400	Enhancers	Liver	Liver
26	chr5:1882400-1883400	Weak transcription	Pancreas	Pancrea
27	chr5:1882400-1883600	Active TSS	Right Atrium	heart
28	chr5:1882400-1884000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr5:1882400-1884200	Bivalent Enhancer	Placenta	Placenta
30	chr5:1882400-1884600	Bivalent Enhancer	Lung	lung
31	chr5:1882400-1884800	Bivalent Enhancer	Spleen	Spleen
32	chr5:1882400-1885400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr5:1882400-1887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:1882400-1887600	Active TSS	NHEK	skin
35	chr5:1882400-1887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:1882600-1883000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr5:1882600-1883000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:1882600-1883000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:1882600-1883000	Bivalent/Poised TSS	Thymus	Thymus
40	chr5:1882600-1883200	Flanking Bivalent TSS/Enh	Ovary	ovary
41	chr5:1882600-1883400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
42	chr5:1882600-1883600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
43	chr5:1882600-1883800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
44	chr5:1882600-1884200	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr5:1882600-1884400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:1882600-1884400	Bivalent/Poised TSS	A549	lung
47	chr5:1882600-1884600	Active TSS	Left Ventricle	heart
48	chr5:1882600-1885000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:1882800-1883000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:1882800-1883000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived

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