Variant report

Variant	rs10473306
Chromosome Location	chr5:43287437-43287438
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43286563-43288171	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:43286219-43288215	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:43284787-43292154	K562	blood:	n/a	n/a
4	POLR2A	chr5:43286673-43287541	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:43286548-43287918	GM12891	blood:	n/a	n/a
6	CCNT2	chr5:43287176-43287581	K562	blood:	n/a	n/a
7	POLR2A	chr5:43286213-43289153	K562	blood:	n/a	n/a
8	POLR2A	chr5:43284759-43289759	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:43285561-43289251	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:43285678-43288190	A549	lung:	n/a	n/a
11	POLR2A	chr5:43284900-43292074	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:43285373-43287718	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr5:43287221-43287438	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:43285987-43287626	GM12878	blood:	n/a	n/a
15	FOSL2	chr5:43285542-43288202	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:43285520-43288419	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:43286539-43288220	K562	blood:	n/a	n/a
18	POLR2A	chr5:43286182-43288228	PBDE	blood:	n/a	n/a
19	HEY1	chr5:43286042-43288237	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:43286303-43288247	K562	blood:	n/a	n/a
21	CHD2	chr5:43286763-43287478	K562	blood:	n/a	n/a
22	POLR2A	chr5:43286268-43288253	K562	blood:	n/a	n/a
23	POLR2A	chr5:43286155-43288219	HL-60	blood:	n/a	n/a
24	POLR2A	chr5:43286190-43289185	HepG2	liver:	n/a	n/a
25	POLR2A	chr5:43287293-43288581	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:43286672-43287467	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr5:43285092-43289217	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:43287341-43287937	GM12892	blood:	n/a	n/a
29	POLR2A	chr5:43286594-43288171	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:43284491-43289202	GM12891	blood:	n/a	n/a
31	POLR2A	chr5:43286110-43288242	GM12878	blood:	n/a	n/a
32	NFATC1	chr5:43287121-43287536	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:43286643-43287550	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr5:43286171-43288245	HL-60	blood:	n/a	n/a
35	POLR2A	chr5:43286715-43288211	HepG2	liver:	n/a	n/a
36	MBD4	chr5:43285040-43288076	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43284931..43287832-chr5:43292804..43295687,2	MCF-7	breast:
2	chr5:43065277..43067135-chr5:43287276..43290196,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261604	TF binding region
ENSG00000112972	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10037409	0.86[EUR][1000 genomes]
rs10037706	1.00[CEU][hapmap]
rs10038859	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10040897	0.86[EUR][1000 genomes]
rs10043148	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs10052384	0.86[EUR][1000 genomes]
rs10054415	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10056437	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10062031	0.86[EUR][1000 genomes]
rs10062121	0.86[EUR][1000 genomes]
rs10062598	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10064967	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10067763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10069507	1.00[CEU][hapmap]
rs10077324	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10079530	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473308	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs11955467	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1478436	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16874093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16874094	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28450849	0.86[EUR][1000 genomes]
rs28608156	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28856961	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4326149	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55645370	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60520238	1.00[EUR][1000 genomes]
rs6865440	0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs6884349	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6892413	0.86[EUR][1000 genomes]
rs6893898	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6895237	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs7356654	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73751075	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751078	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73751082	0.86[EUR][1000 genomes]
rs73751083	0.86[EUR][1000 genomes]
rs7710717	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7715267	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729140	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7729145	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7733732	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9292869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292870	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs9292872	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292875	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
4	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43282800-43292800	Weak transcription	Hela-S3	cervix
2	chr5:43283400-43287600	Weak transcription	NH-A	brain
3	chr5:43283600-43287600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:43284000-43287600	Weak transcription	NHEK	skin
5	chr5:43284200-43294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:43284600-43287800	Weak transcription	HepG2	liver
8	chr5:43284800-43287800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:43284800-43289000	Weak transcription	Small Intestine	intestine
10	chr5:43285000-43287800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:43285000-43288200	Strong transcription	A549	lung
12	chr5:43285000-43291400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:43285000-43291400	Weak transcription	Osteobl	bone
14	chr5:43285000-43293400	Weak transcription	Pancreas	Pancrea
15	chr5:43285000-43300800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:43285200-43294200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:43285400-43287800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:43285400-43290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:43285400-43291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:43285400-43291600	Weak transcription	Fetal Kidney	kidney
21	chr5:43285400-43292000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:43285400-43292600	Weak transcription	Fetal Brain Male	brain
23	chr5:43285600-43290200	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:43285600-43291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:43285600-43293400	Weak transcription	Colonic Mucosa	Colon
26	chr5:43285600-43300000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:43285600-43302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:43285600-43302800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr5:43285800-43289000	Strong transcription	Primary T cells from cord blood	blood
30	chr5:43285800-43291800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:43286200-43288400	Strong transcription	Brain Germinal Matrix	brain
32	chr5:43286200-43288800	Strong transcription	HSMM	muscle
33	chr5:43286200-43291600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:43286200-43295600	Strong transcription	HSMMtube	muscle
35	chr5:43286200-43298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:43286200-43300600	Strong transcription	Fetal Intestine Large	intestine
37	chr5:43286400-43288200	Strong transcription	Brain Angular Gyrus	brain
38	chr5:43286400-43288200	Strong transcription	Fetal Stomach	stomach
39	chr5:43286400-43288800	Strong transcription	Adipose Nuclei	Adipose
40	chr5:43286400-43288800	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:43286400-43289000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:43286400-43289200	Enhancers	Fetal Heart	heart
43	chr5:43286400-43289200	Strong transcription	Placenta	Placenta
44	chr5:43286400-43289600	Strong transcription	Fetal Brain Female	brain
45	chr5:43286400-43290400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:43286400-43290400	Weak transcription	Ovary	ovary
47	chr5:43286400-43291200	Strong transcription	NHLF	lung
48	chr5:43286400-43302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:43286400-43302400	Strong transcription	GM12878-XiMat	blood
50	chr5:43286600-43288000	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links