Variant report

Variant	rs62406228
Chromosome Location	chr5:179238251-179238252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr5:179238220-179238897	K562	blood:	n/a	n/a
2	POLR2A	chr5:179238226-179238811	K562	blood:	n/a	n/a
3	POLR2A	chr5:179238167-179238584	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr5:179238106-179238919	K562	blood:	n/a	n/a
5	IRF1	chr5:179238188-179238703	K562	blood:	n/a	n/a
6	POLR2A	chr5:179238161-179238578	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr5:179238196-179238569	Hela-S3	cervix:	n/a	n/a
8	ZNF143	chr5:179238224-179238667	K562	blood:	n/a	n/a
9	POU2F2	chr5:179238167-179238537	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:179238132-179238899	K562	blood:	n/a	n/a
11	POLR2A	chr5:179238194-179238876	K562	blood:	n/a	n/a
12	PML	chr5:179238236-179238915	K562	blood:	n/a	n/a
13	SP4	chr5:179238181-179238552	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:179238120-179238386	HepG2	liver:	n/a	n/a
15	TEAD4	chr5:179238190-179238787	K562	blood:	n/a	n/a
16	POLR2A	chr5:179238188-179238890	K562	blood:	n/a	n/a
17	MAX	chr5:179238226-179238519	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAZ	chr5:179238249-179238848	K562	blood:	n/a	n/a
19	POLR2A	chr5:179238101-179238967	K562	blood:	n/a	n/a
20	CBX3	chr5:179238100-179238861	K562	blood:	n/a	n/a
21	TAF1	chr5:179238224-179238888	K562	blood:	n/a	n/a
22	HEY1	chr5:179238237-179238678	K562	blood:	n/a	n/a
23	ZNF384	chr5:179238074-179238772	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
SQSTM1	TF binding region
MGAT4B	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11738269	0.82[AMR][1000 genomes]
rs11739042	0.82[AMR][1000 genomes]
rs11741570	0.81[AMR][1000 genomes]
rs11744616	0.83[AMR][1000 genomes]
rs1469020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1469021	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3797776	0.83[AMR][1000 genomes]
rs41458244	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4700838	0.81[AMR][1000 genomes]
rs4700840	0.81[AMR][1000 genomes]
rs55827522	0.82[AMR][1000 genomes]
rs56335144	0.81[AMR][1000 genomes]
rs62406187	0.82[AMR][1000 genomes]
rs62406223	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62406227	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406229	0.99[ASN][1000 genomes]
rs72807339	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs730012	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7444006	0.81[AMR][1000 genomes]
rs7447159	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
10	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
11	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
12	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
13	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
14	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	158 gene(s)	inside rSNPs	diseases
15	nsv883285	chr5:179223023-179238794	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	153 gene(s)	inside rSNPs	diseases
16	nsv600668	chr5:179227865-179242581	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv988291	chr5:179233076-179240737	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
19	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179233400-179244400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:179234400-179243800	Weak transcription	Aorta	Aorta
3	chr5:179234600-179238400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:179234600-179238400	Weak transcription	K562	blood
5	chr5:179234600-179239000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179234600-179239200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179234600-179239200	Weak transcription	Brain Anterior Caudate	brain
8	chr5:179234600-179239200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:179234600-179239200	Weak transcription	Ovary	ovary
10	chr5:179234600-179239200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:179234600-179239200	Weak transcription	NHLF	lung
12	chr5:179234600-179239400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:179234600-179239400	Weak transcription	Primary T cells from cord blood	blood
14	chr5:179234600-179241000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:179234600-179241000	Weak transcription	Fetal Lung	lung
16	chr5:179234600-179241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:179234600-179242800	Weak transcription	Esophagus	oesophagus
18	chr5:179234600-179242800	Weak transcription	Gastric	stomach
19	chr5:179234600-179243600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:179234600-179243600	Weak transcription	Brain Substantia Nigra	brain
21	chr5:179234600-179243600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:179234600-179243800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:179234600-179244000	Weak transcription	NHDF-Ad	bronchial
24	chr5:179234600-179244200	Weak transcription	NHEK	skin
25	chr5:179234600-179245200	Weak transcription	HSMMtube	muscle
26	chr5:179234600-179245800	Weak transcription	Fetal Kidney	kidney
27	chr5:179234800-179238600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:179234800-179238600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:179234800-179238600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:179234800-179239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:179234800-179239000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:179234800-179239200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:179234800-179239200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:179234800-179239400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:179234800-179239400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:179234800-179243600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:179234800-179243600	Weak transcription	Brain Angular Gyrus	brain
38	chr5:179234800-179243600	Weak transcription	Osteobl	bone
39	chr5:179235000-179239200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:179235000-179240000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:179235000-179241400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:179235000-179243600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:179235000-179243600	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:179235000-179243600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:179235200-179238600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:179235200-179238600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:179235200-179238600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:179235200-179239200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:179235200-179239200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:179235200-179239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links