Variant report

Variant	rs58225020
Chromosome Location	chr5:179246784-179246785
allele	C/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	POLR2A	chr5:179245684-179255371	K562	blood:	n/a	n/a
2	MXI1	chr5:179245669-179247068	GM12878	blood:	n/a	chr5:179246557-179246566 chr5:179246128-179246137 chr5:179246557-179246566 chr5:179246559-179246568
3	MAX	chr5:179245573-179249061	ECC-1	luminal epithelium:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179247807-179247817 chr5:179246553-179246572 chr5:179246558-179246567 chr5:179247553-179247562
4	POLR2A	chr5:179245036-179249094	K562	blood:	n/a	n/a
5	POLR2A	chr5:179245250-179250058	GM12878	blood:	n/a	n/a
6	MAX	chr5:179245655-179246962	H1-hESC	embryonic stem cell:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179246553-179246572 chr5:179246558-179246567
7	SMARCB1	chr5:179245170-179249011	Hela-S3	cervix:	n/a	chr5:179246108-179246117 chr5:179246586-179246595
8	NFATC1	chr5:179246564-179247184	GM12878	blood:	n/a	n/a
9	BCL3	chr5:179245033-179248254	A549	lung:	n/a	chr5:179248153-179248166 chr5:179246322-179246335 chr5:179248150-179248163 chr5:179246136-179246145 chr5:179245888-179245901 chr5:179246140-179246153 chr5:179245784-179245793 chr5:179248191-179248204 chr5:179246224-179246237 chr5:179246174-179246183 chr5:179248158-179248167
10	POLR2A	chr5:179246352-179246802	HepG2	liver:	n/a	n/a
11	MAX	chr5:179245628-179249027	A549	lung:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179247807-179247817 chr5:179246553-179246572 chr5:179246558-179246567 chr5:179247553-179247562
12	RFX5	chr5:179245918-179247199	HepG2	liver:	n/a	n/a
13	MYC	chr5:179245779-179246796	NB4	blood:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179246553-179246572 chr5:179246558-179246567
14	CHD2	chr5:179245947-179246787	K562	blood:	n/a	chr5:179246143-179246153 chr5:179246320-179246330
15	USF1	chr5:179246358-179246825	A549	lung:	n/a	chr5:179246556-179246567
16	POLR2A	chr5:179245372-179249674	GM19099	blood:	n/a	n/a
17	HCFC1	chr5:179245195-179249527	Hela-S3	cervix:	n/a	n/a
18	NR3C1	chr5:179245870-179246814	A549	lung:	n/a	chr5:179246642-179246655 chr5:179246585-179246594 chr5:179246033-179246048 chr5:179246107-179246116
19	TCF12	chr5:179245210-179250266	A549	lung:	n/a	chr5:179248789-179248799 chr5:179246679-179246689 chr5:179249700-179249710 chr5:179249664-179249671 chr5:179249663-179249673
20	GATA3	chr5:179245544-179246996	A549	lung:	n/a	n/a
21	EGR1	chr5:179246543-179247172	ECC-1	luminal epithelium:	n/a	chr5:179246838-179246849
22	SIN3A	chr5:179245385-179247005	H1-hESC	embryonic stem cell:	n/a	chr5:179246826-179246837 chr5:179246217-179246228 chr5:179246595-179246608 chr5:179246559-179246568 chr5:179246557-179246566
23	PBX3	chr5:179245840-179246802	A549	lung:	n/a	n/a
24	ZKSCAN1	chr5:179245699-179247511	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr5:179246687-179246936	MCF10A-Er-Src	breast:	n/a	n/a
26	MYC	chr5:179246425-179246795	GM12878	blood:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246557-179246568 chr5:179246553-179246572 chr5:179246558-179246567
27	POLR2A	chr5:179245482-179249019	HL-60	blood:	n/a	n/a
28	CTBP2	chr5:179245827-179248892	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr5:179245790-179247005	Hela-S3	cervix:	n/a	chr5:179246557-179246566 chr5:179246128-179246137 chr5:179246557-179246566 chr5:179246559-179246568
30	USF2	chr5:179245887-179246872	GM12878	blood:	n/a	chr5:179246125-179246136
31	CREB1	chr5:179245742-179246818	H1-hESC	embryonic stem cell:	n/a	n/a
32	EP300	chr5:179245723-179246881	SK-N-SH	brain:	n/a	chr5:179246543-179246559 chr5:179245779-179245793 chr5:179246225-179246241
33	EP300	chr5:179245507-179246883	A549	lung:	n/a	chr5:179246543-179246559 chr5:179245779-179245793 chr5:179246225-179246241
34	MAX	chr5:179245590-179247417	GM12878	blood:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179246553-179246572 chr5:179246558-179246567
35	CHD2	chr5:179245836-179247043	Hela-S3	cervix:	n/a	chr5:179246143-179246153 chr5:179246320-179246330
36	POLR2A	chr5:179244943-179253663	PANC-1	pancreas:	n/a	n/a
37	TFAP2C	chr5:179245652-179248819	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr5:179246432-179248262	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:179245675-179253142	IMR90	lung:	n/a	n/a
40	EP300	chr5:179245754-179246966	K562	blood:	n/a	chr5:179246543-179246559 chr5:179245779-179245793 chr5:179246225-179246241
41	EBF1	chr5:179246698-179247052	GM12878	blood:	n/a	chr5:179246903-179246914 chr5:179246904-179246914 chr5:179246905-179246914
42	CTCF	chr5:179246476-179246805	GM12878	blood:	n/a	n/a
43	JUND	chr5:179245703-179247002	K562	blood:	n/a	chr5:179246586-179246594 chr5:179246324-179246333 chr5:179246327-179246336 chr5:179246107-179246117 chr5:179246108-179246116 chr5:179246951-179246958 chr5:179246584-179246596 chr5:179246107-179246117 chr5:179246326-179246335 chr5:179246106-179246118 chr5:179246585-179246595 chr5:179246106-179246117 chr5:179246323-179246332
44	USF1	chr5:179245809-179246786	H1-hESC	embryonic stem cell:	n/a	chr5:179246126-179246137 chr5:179246556-179246567
45	MAX	chr5:179245831-179246849	SK-N-SH	brain:	n/a	chr5:179246557-179246568 chr5:179246558-179246568 chr5:179246557-179246568 chr5:179246557-179246567 chr5:179246556-179246569 chr5:179246328-179246338 chr5:179246557-179246567 chr5:179246558-179246568 chr5:179246556-179246569 chr5:179246556-179246569 chr5:179246211-179246220 chr5:179246557-179246568 chr5:179246553-179246572 chr5:179246558-179246567
46	PAX5	chr5:179246353-179246973	GM12878	blood:	n/a	chr5:179246854-179246872 chr5:179246590-179246599
47	RELA	chr5:179245711-179247024	GM18951	blood:	n/a	n/a
48	POLR2A	chr5:179245155-179248947	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:179246775-179246824	MCF-7	breast:	n/a	n/a
50	POLR2A	chr5:179245228-179249128	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:39715244..39717171-chr5:179246007..179248783,2	MCF-7	breast:
2	chr5:179158644..179160831-chr5:179243809..179247207,3	K562	blood:
3	chr5:179124982..179127073-chr5:179245665..179248620,3	MCF-7	breast:
4	chr5:179047278..179052613-chr5:179246048..179251997,13	K562	blood:
5	chr5:179245762..179250347-chr5:179281858..179288397,17	MCF-7	breast:
6	chr5:179049088..179052063-chr5:179245796..179250145,6	MCF-7	breast:
7	chr5:178975834..178978833-chr5:179245271..179247079,2	K562	blood:
8	chr5:179122850..179128148-chr5:179246584..179249342,5	K562	blood:
9	chr5:179246365..179250489-chr5:179281961..179288216,8	MCF-7	breast:
10	chr5:179159613..179162067-chr5:179246269..179249324,3	MCF-7	breast:
11	chr5:179157089..179164271-chr5:179242384..179250347,16	K562	blood:
12	chr5:179246544..179252042-chr5:179284250..179287282,6	K562	blood:
13	chr5:179157063..179161797-chr5:179244181..179249709,13	MCF-7	breast:
14	chr3:113415039..113416819-chr5:179245947..179248252,2	MCF-7	breast:
15	chr5:179124597..179127055-chr5:179246139..179249577,4	MCF-7	breast:
16	chr5:179245622..179247689-chr5:179288276..179289796,2	MCF-7	breast:
17	chr5:179246093..179248273-chr5:179497691..179500264,2	MCF-7	breast:
18	chr5:179244299..179249031-chr5:179283718..179288072,6	K562	blood:
19	chr5:179047831..179051506-chr5:179245810..179250436,9	MCF-7	breast:
20	chr5:179047637..179052326-chr5:179245599..179249536,7	K562	blood:
21	chr5:179047327..179049016-chr5:179246235..179248894,2	MCF-7	breast:
22	chr5:179246564..179250154-chr5:179266751..179272341,6	MCF-7	breast:
23	chr5:179190822..179197512-chr5:179244986..179249382,7	K562	blood:

Variant related genes	Relation type
SQSTM1	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000176542	Chromatin interaction
ENSG00000100316	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000245317	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10040357	1.00[EUR][1000 genomes]
rs10058037	1.00[EUR][1000 genomes]
rs11743197	1.00[EUR][1000 genomes]
rs13356823	1.00[EUR][1000 genomes]
rs13358321	1.00[EUR][1000 genomes]
rs156099	1.00[EUR][1000 genomes]
rs17079679	1.00[EUR][1000 genomes]
rs1960428	1.00[EUR][1000 genomes]
rs269459	1.00[EUR][1000 genomes]
rs269460	1.00[EUR][1000 genomes]
rs28656195	1.00[EUR][1000 genomes]
rs4438838	1.00[EUR][1000 genomes]
rs56844432	1.00[EUR][1000 genomes]
rs57000847	1.00[EUR][1000 genomes]
rs57104438	1.00[EUR][1000 genomes]
rs58007232	1.00[EUR][1000 genomes]
rs58586529	1.00[EUR][1000 genomes]
rs58899481	1.00[EUR][1000 genomes]
rs60407359	1.00[EUR][1000 genomes]
rs60822577	1.00[EUR][1000 genomes]
rs61330504	1.00[EUR][1000 genomes]
rs6863030	1.00[EUR][1000 genomes]
rs6872508	1.00[EUR][1000 genomes]
rs73810492	1.00[EUR][1000 genomes]
rs73810493	1.00[EUR][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	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	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
11	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
12	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
13	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179243000-179246800	Weak transcription	Dnd41	blood
2	chr5:179243400-179247200	Enhancers	Spleen	Spleen
3	chr5:179243600-179246800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr5:179244400-179247000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:179244400-179247000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:179244400-179247800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179244600-179247400	Enhancers	HUVEC	blood vessel
8	chr5:179245000-179247800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179245000-179247800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr5:179245000-179247800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:179245200-179247600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:179245200-179247600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:179245200-179247600	Enhancers	HMEC	breast
14	chr5:179245200-179247800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:179245200-179247800	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr5:179245200-179247800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr5:179245400-179246800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179245400-179246800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr5:179245400-179247600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:179245400-179247600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:179245400-179247800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179245400-179247800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr5:179245400-179247800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr5:179245400-179247800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:179245400-179247800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr5:179245400-179247800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:179245400-179248600	Enhancers	Fetal Brain Male	brain
28	chr5:179245600-179246800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:179245600-179246800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr5:179245600-179247000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr5:179245600-179247800	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr5:179245600-179247800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:179245600-179247800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr5:179245600-179247800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:179245800-179247400	Enhancers	NHEK	skin
36	chr5:179245800-179247800	Flanking Active TSS	HSMM	muscle
37	chr5:179246000-179247000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr5:179246000-179247200	Enhancers	Fetal Heart	heart
39	chr5:179246000-179247200	Enhancers	Gastric	stomach
40	chr5:179246000-179247200	Weak transcription	Small Intestine	intestine
41	chr5:179246000-179247400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:179246000-179247400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:179246000-179247600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:179246200-179246800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr5:179246200-179246800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:179246200-179246800	Enhancers	Primary T cells from cord blood	blood
47	chr5:179246200-179246800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr5:179246200-179246800	Weak transcription	Fetal Kidney	kidney
49	chr5:179246200-179246800	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr5:179246200-179246800	Enhancers	Lung	lung

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