Variant report

Variant	rs58413676
Chromosome Location	chr5:179229151-179229152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:123)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:179228858-179229201	K562	blood:	n/a	n/a
2	IRF4	chr5:179228767-179229177	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:179228800-179231391	K562	blood:	n/a	n/a
4	YY1	chr5:179228799-179229170	GM12878	blood:	n/a	n/a
5	RAD21	chr5:179228752-179229209	HepG2	liver:	n/a	n/a
6	MAX	chr5:179228770-179229232	A549	lung:	n/a	n/a
7	MAX	chr5:179228713-179229168	H1-hESC	embryonic stem cell:	n/a	n/a
8	SMC3	chr5:179228867-179229234	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:179228149-179229233	MCF-7	breast:	n/a	n/a
10	RAD21	chr5:179228820-179229205	A549	lung:	n/a	n/a
11	RAD21	chr5:179228851-179229341	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:179228764-179229233	GM12892	blood:	n/a	n/a
13	CTCF	chr5:179228857-179229291	K562	blood:	n/a	chr5:179229196-179229205
14	USF1	chr5:179228844-179229231	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:179228692-179229348	PANC-1	pancreas:	n/a	n/a
16	SMC3	chr5:179228750-179229589	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr5:179228642-179229262	HCT-116	colon:	n/a	chr5:179229196-179229205
18	RAD21	chr5:179228727-179229427	HCT-116	colon:	n/a	chr5:179229358-179229372
19	POLR2A	chr5:179228870-179229192	HCT-116	colon:	n/a	n/a
20	MTA3	chr5:179228784-179229339	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:179228636-179229280	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr5:179228182-179229253	GM12878	blood:	n/a	n/a
23	CTCF	chr5:179228405-179229422	A549	lung:	n/a	chr5:179229354-179229367 chr5:179229196-179229205
24	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
25	CTCF	chr5:179228746-179229205	H1-hESC	embryonic stem cell:	n/a	chr5:179229196-179229205
26	POLR2A	chr5:179228739-179229166	GM12892	blood:	n/a	n/a
27	USF2	chr5:179228917-179229174	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:179227663-179229654	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr5:179228765-179229433	GM12891	blood:	n/a	n/a
30	POLR2A	chr5:179228118-179229843	HL-60	blood:	n/a	n/a
31	USF1	chr5:179228868-179229246	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr5:179228779-179229232	GM12878	blood:	n/a	chr5:179229196-179229205
33	MAX	chr5:179228852-179229208	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:179228463-179229544	A549	lung:	n/a	n/a
35	RAD21	chr5:179228834-179229264	A549	lung:	n/a	n/a
36	CTCF	chr5:179228826-179229157	Spleen_OC	spleen:	n/a	n/a
37	BCLAF1	chr5:179228755-179229209	GM12878	blood:	n/a	n/a
38	RAD21	chr5:179228830-179229194	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr5:179228773-179229290	PANC-1	pancreas:	n/a	n/a
40	RAD21	chr5:179228791-179229180	HepG2	liver:	n/a	n/a
41	RAD21	chr5:179228820-179229202	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr5:179228771-179229195	K562	blood:	n/a	n/a
43	POLR2A	chr5:179228977-179229303	HepG2	liver:	n/a	n/a
44	RAD21	chr5:179228768-179229168	H1-hESC	embryonic stem cell:	n/a	n/a
45	POU2F2	chr5:179228767-179229210	GM12878	blood:	n/a	n/a
46	MXI1	chr5:179228863-179229235	GM12878	blood:	n/a	n/a
47	USF1	chr5:179228880-179229200	A549	lung:	n/a	n/a
48	RAD21	chr5:179228749-179229283	A549	lung:	n/a	n/a
49	USF1	chr5:179228876-179229240	A549	lung:	n/a	n/a
50	MAX	chr5:179228832-179229259	NB4	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179227703..179229883-chr5:179285735..179289127,3	K562	blood:
2	chr5:179125163..179127622-chr5:179228110..179231035,2	K562	blood:
3	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
4	chr5:179227831..179231343-chr5:179333679..179336075,3	MCF-7	breast:
5	chr5:179227703..179229883-chr5:179285735..179288229,2	K562	blood:
6	chr5:179159678..179161359-chr5:179228559..179231556,2	MCF-7	breast:
7	chr5:179197599..179200377-chr5:179228822..179231191,2	MCF-7	breast:

No data

Variant related genes	Relation type
MGAT4B	TF binding region
MIR1229	TF binding region
SQSTM1	TF binding region
ENSG00000161010	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000245317	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs58773990	0.87[EUR][1000 genomes]
rs73351608	0.87[EUR][1000 genomes]
rs73351610	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73351620	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	149 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv600662	chr5:179220010-179231248	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
15	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
16	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
17	nsv883282	chr5:179220638-179231248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
18	nsv883283	chr5:179220638-179231681	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
19	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
20	nsv600665	chr5:179221789-179231248	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
21	nsv600666	chr5:179221789-179231681	Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
22	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
23	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179223800-179229600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179223800-179231600	Weak transcription	Fetal Kidney	kidney
3	chr5:179223800-179231600	Weak transcription	Psoas Muscle	Psoas
4	chr5:179224000-179229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:179224000-179229200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:179224000-179229200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:179224000-179229400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:179224000-179229600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:179224000-179230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:179224000-179230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:179224000-179230000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:179224000-179230800	Weak transcription	Right Atrium	heart
13	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:179224200-179229600	Weak transcription	NH-A	brain
15	chr5:179224200-179230000	Strong transcription	Brain Germinal Matrix	brain
16	chr5:179224400-179229200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:179224400-179229200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:179224400-179229200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr5:179224400-179229600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:179225400-179229200	Strong transcription	Fetal Intestine Large	intestine
21	chr5:179226200-179232200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:179226800-179233200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:179227000-179229400	Weak transcription	Primary B cells from cord blood	blood
24	chr5:179227000-179230800	Weak transcription	Fetal Brain Male	brain
25	chr5:179227200-179230200	Weak transcription	HUVEC	blood vessel
26	chr5:179227200-179231000	Weak transcription	HSMMtube	muscle
27	chr5:179227200-179231800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:179227400-179230200	Weak transcription	Thymus	Thymus
29	chr5:179227600-179229200	Weak transcription	Brain Angular Gyrus	brain
30	chr5:179227600-179230000	Weak transcription	Primary T cells from cord blood	blood
31	chr5:179227600-179230000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:179227600-179230000	Weak transcription	HSMM	muscle
33	chr5:179227600-179230200	Weak transcription	Fetal Lung	lung
34	chr5:179227600-179232000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:179227800-179229400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:179227800-179232000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:179227800-179232200	Enhancers	Fetal Heart	heart
38	chr5:179228000-179229600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:179228000-179229800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:179228000-179230800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr5:179228000-179231200	Weak transcription	Brain Anterior Caudate	brain
42	chr5:179228000-179232400	Weak transcription	Aorta	Aorta
43	chr5:179228200-179229800	Weak transcription	NHEK	skin
44	chr5:179228200-179230200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:179228400-179229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:179228400-179229200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:179228400-179229200	Weak transcription	HepG2	liver
48	chr5:179228400-179229400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:179228400-179229600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:179228400-179229600	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links