Variant report

Variant	rs58254276
Chromosome Location	chr5:112539311-112539312
allele	A/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	MYC	chr5:112538869-112539334	K562	blood:	n/a	n/a
2	POLR2A	chr5:112538729-112539576	U87	brain:	n/a	n/a
3	FOS	chr5:112538839-112539445	MCF10A-Er-Src	breast:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539051-112539061
4	KAP1	chr5:112538696-112539860	U2OS	brain:	n/a	chr5:112538767-112538775
5	MAX	chr5:112538489-112539551	HCT-116	colon:	n/a	n/a
6	FOXA2	chr5:112539042-112539374	HepG2	liver:	n/a	n/a
7	EP300	chr5:112538855-112539322	HepG2	liver:	n/a	n/a
8	RCOR1	chr5:112538892-112539399	K562	blood:	n/a	n/a
9	POLR2A	chr5:112538518-112539877	PFSK-1	brain:	n/a	n/a
10	MYC	chr5:112538713-112539316	MCF10A-Er-Src	breast:	n/a	n/a
11	SP1	chr5:112538586-112539545	HCT-116	colon:	n/a	chr5:112539065-112539079
12	MXI1	chr5:112537418-112540905	SK-N-SH	brain:	n/a	n/a
13	ZNF263	chr5:112538624-112539530	HEK293-T-REx	kidney:	n/a	n/a
14	GATA3	chr5:112539138-112539618	SH-SY5Y	brain:	n/a	chr5:112539149-112539162 chr5:112539147-112539163 chr5:112539144-112539165
15	CBX3	chr5:112538745-112539426	HCT-116	colon:	n/a	n/a
16	EP300	chr5:112538883-112539343	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr5:112538729-112539538	U87	brain:	n/a	n/a
18	REST	chr5:112538886-112539398	PFSK-1	brain:	n/a	chr5:112539059-112539068 chr5:112539123-112539131 chr5:112539059-112539066 chr5:112539062-112539075
19	TCF7L2	chr5:112538752-112539682	HEK293	kidney:	n/a	n/a
20	MAX	chr5:112538684-112539371	K562	blood:	n/a	n/a
21	NR2F2	chr5:112538954-112539387	K562	blood:	n/a	n/a
22	MAX	chr5:112538543-112539414	HCT-116	colon:	n/a	n/a
23	SIN3AK20	chr5:112538614-112539469	HCT-116	colon:	n/a	n/a
24	SP1	chr5:112538424-112539582	HCT-116	colon:	n/a	chr5:112539065-112539079
25	JUND	chr5:112538582-112539470	HCT-116	colon:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539061 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539051-112539061
26	RCOR1	chr5:112538929-112539364	K562	blood:	n/a	n/a
27	MYC	chr5:112538089-112539636	MCF10A-Er-Src	breast:	n/a	n/a
28	GATA2	chr5:112538900-112539914	SH-SY5Y	brain:	n/a	chr5:112539149-112539162 chr5:112539147-112539163 chr5:112539144-112539165
29	TEAD4	chr5:112539028-112539347	HepG2	liver:	n/a	n/a
30	MXI1	chr5:112538629-112539546	IMR90	lung:	n/a	n/a
31	EP300	chr5:112538047-112541128	SK-N-SH	brain:	n/a	chr5:112540678-112540691
32	POLR2A	chr5:112538654-112539409	U87	brain:	n/a	n/a
33	KAP1	chr5:112538726-112540002	HEK293	kidney:	n/a	chr5:112538767-112538775
34	POLR2A	chr5:112538508-112539414	PFSK-1	brain:	n/a	n/a
35	CUX1	chr5:112539010-112539353	K562	blood:	n/a	n/a
36	FOS	chr5:112538841-112539628	MCF10A-Er-Src	breast:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539051-112539061
37	JUND	chr5:112538552-112539456	HCT-116	colon:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539061 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539051-112539061
38	FOSL1	chr5:112538576-112539518	HCT-116	colon:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539050-112539061 chr5:112539051-112539061
39	FOSL1	chr5:112538749-112539524	HCT-116	colon:	n/a	chr5:112539051-112539061 chr5:112539052-112539060 chr5:112539050-112539062 chr5:112539051-112539061 chr5:112539050-112539061 chr5:112539051-112539061
40	USF1	chr5:112538665-112539458	HCT-116	colon:	n/a	chr5:112539113-112539124
41	POLR2A	chr5:112538723-112539480	MCF10A-Er-Src	breast:	n/a	n/a
42	SETDB1	chr5:112539009-112539383	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112537173..112539985-chr5:112540177..112543162,2	K562	blood:
2	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region
ENSG00000047188	Chromatin interaction
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs34086862	1.00[EUR][1000 genomes]
rs6878004	1.00[EUR][1000 genomes]
rs73244739	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73244745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73244746	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73244747	1.00[EUR][1000 genomes]
rs73244748	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73244750	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112522600-112541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:112531800-112541000	Weak transcription	Aorta	Aorta
3	chr5:112533800-112541400	Weak transcription	Spleen	Spleen
4	chr5:112535600-112540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:112535600-112540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:112535800-112540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:112536200-112540200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:112536400-112541800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:112537000-112540400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112537200-112541800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:112537200-112542000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:112537400-112539400	Enhancers	HUVEC	blood vessel
13	chr5:112537400-112541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr5:112537400-112541800	Enhancers	Adipose Nuclei	Adipose
15	chr5:112537600-112539400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:112537600-112539400	Enhancers	Ovary	ovary
17	chr5:112537600-112539400	Enhancers	Psoas Muscle	Psoas
18	chr5:112537600-112540000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:112537600-112541200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:112538000-112539800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:112538000-112541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:112538200-112539400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr5:112538400-112540400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:112538400-112541000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:112538400-112541200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:112538600-112539400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:112538600-112539400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:112538600-112539400	Flanking Active TSS	Fetal Lung	lung
29	chr5:112538600-112539400	Enhancers	Fetal Stomach	stomach
30	chr5:112538600-112539400	Flanking Active TSS	NH-A	brain
31	chr5:112538600-112539600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:112538600-112539600	Active TSS	Brain Germinal Matrix	brain
33	chr5:112538600-112539600	Enhancers	Stomach Mucosa	stomach
34	chr5:112538600-112540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:112538600-112540000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:112538600-112540000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:112538600-112540400	Flanking Active TSS	NHEK	skin
38	chr5:112538600-112541800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:112538600-112542000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:112538800-112539400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:112538800-112539400	Flanking Active TSS	Right Atrium	heart
42	chr5:112538800-112539400	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr5:112538800-112539400	Flanking Bivalent TSS/Enh	K562	blood
44	chr5:112538800-112539600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr5:112538800-112539800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:112538800-112540000	Active TSS	Esophagus	oesophagus
47	chr5:112538800-112541800	Enhancers	Brain Cingulate Gyrus	brain
48	chr5:112538800-112542000	Enhancers	HMEC	breast
49	chr5:112538800-112544200	Weak transcription	Fetal Kidney	kidney
50	chr5:112539000-112539400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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