Variant report

Variant	rs58646811
Chromosome Location	chr5:179758962-179758963
allele	G/T
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	MAX	chr5:179758654-179759310	H1-hESC	embryonic stem cell:	n/a	chr5:179759234-179759244
2	TEAD4	chr5:179758860-179759434	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr5:179758906-179759387	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr5:179758769-179759532	ECC-1	luminal epithelium:	n/a	chr5:179759178-179759194
5	RAD21	chr5:179758651-179759561	H1-hESC	embryonic stem cell:	n/a	n/a
6	RFX5	chr5:179758770-179759238	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr5:179758560-179759353	H1-hESC	embryonic stem cell:	n/a	chr5:179759178-179759194
8	EP300	chr5:179758851-179759261	ECC-1	luminal epithelium:	n/a	chr5:179759178-179759194
9	TBP	chr5:179758636-179759115	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr5:179758711-179759122	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr5:179758390-179759277	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr5:179758923-179759230	H1-hESC	embryonic stem cell:	n/a	chr5:179758925-179758933
13	ATF2	chr5:179758507-179759265	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOSL2	chr5:179757411-179759207	A549	lung:	n/a	chr5:179757999-179758009 chr5:179757998-179758010 chr5:179757999-179758009 chr5:179757999-179758009 chr5:179757996-179758007 chr5:179758000-179758008 chr5:179758416-179758425 chr5:179758099-179758110
15	MAX	chr5:179758911-179759402	ECC-1	luminal epithelium:	n/a	chr5:179759234-179759244
16	TEAD4	chr5:179758559-179759423	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:179757573-179759193	U87	brain:	n/a	n/a
18	EP300	chr5:179758540-179759297	H1-hESC	embryonic stem cell:	n/a	chr5:179759178-179759194
19	SP1	chr5:179758454-179759195	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP1	chr5:179758467-179759220	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr5:179758900-179759312	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:179758548-179759465	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:179755126-179759108	U87	brain:	n/a	n/a
24	POLR2A	chr5:179757573-179759106	U87	brain:	n/a	n/a
25	STAT3	chr5:179757407-179759529	MCF10A-Er-Src	breast:	n/a	chr5:179757830-179757841 chr5:179758243-179758266 chr5:179759242-179759254 chr5:179758258-179758266 chr5:179758255-179758269 chr5:179757872-179757880 chr5:179757956-179757968
26	MAX	chr5:179758915-179759406	H1-hESC	embryonic stem cell:	n/a	chr5:179759234-179759244
27	SIN3A	chr5:179758601-179759373	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr5:179758468-179759234	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr5:179758757-179759386	ECC-1	luminal epithelium:	n/a	n/a
30	NFIC	chr5:179758628-179759388	ECC-1	luminal epithelium:	n/a	n/a
31	BACH1	chr5:179758683-179759306	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZNF143	chr5:179758757-179759481	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr5:179757503-179759416	A549	lung:	n/a	chr5:179759234-179759244
34	E2F6	chr5:179758850-179759401	H1-hESC	embryonic stem cell:	n/a	chr5:179759241-179759250
35	MAX	chr5:179758937-179759408	H1-hESC	embryonic stem cell:	n/a	chr5:179759234-179759244
36	STAT3	chr5:179757527-179759528	MCF10A-Er-Src	breast:	n/a	chr5:179757830-179757841 chr5:179758243-179758266 chr5:179759242-179759254 chr5:179758258-179758266 chr5:179758255-179758269 chr5:179757872-179757880 chr5:179757956-179757968
37	NFIC	chr5:179758808-179759381	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr5:179758557-179759458	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD2	chr5:179758962-179759121	Hela-S3	cervix:	n/a	n/a
40	TCF12	chr5:179758791-179759438	ECC-1	luminal epithelium:	n/a	chr5:179758925-179758933 chr5:179759248-179759258
41	TCF12	chr5:179758940-179759365	H1-hESC	embryonic stem cell:	n/a	chr5:179759248-179759258
42	CEBPB	chr5:179758669-179759437	H1-hESC	embryonic stem cell:	n/a	n/a
43	JUN	chr5:179758954-179759179	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr5:179757556-179759111	IMR90	lung:	n/a	n/a
45	POLR2A	chr5:179758568-179758990	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr5:179757214-179759694	A549	lung:	n/a	n/a
47	MAX	chr5:179758849-179759306	ECC-1	luminal epithelium:	n/a	chr5:179759234-179759244
48	JUND	chr5:179758386-179759449	H1-hESC	embryonic stem cell:	n/a	chr5:179759239-179759248 chr5:179759307-179759319 chr5:179759240-179759249 chr5:179759236-179759245 chr5:179758416-179758425
49	CHD2	chr5:179758598-179759240	H1-hESC	embryonic stem cell:	n/a	n/a
50	MXI1	chr5:179758591-179759166	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179717698..179720150-chr5:179758033..179760822,3	MCF-7	breast:
2	chr5:179720130..179723028-chr5:179758867..179761631,2	MCF-7	breast:
3	chr5:179718232..179719781-chr5:179756949..179759059,2	MCF-7	breast:
4	chr5:179758118..179760214-chr5:179779421..179781494,2	MCF-7	breast:

Variant related genes	Relation type
GFPT2	TF binding region
ENSG00000248367	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000131459	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs58553716	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59738929	1.00[AMR][1000 genomes]
rs6601115	1.00[AMR][1000 genomes]
rs6884111	1.00[AMR][1000 genomes]
rs73811444	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811446	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811447	1.00[AMR][1000 genomes]
rs73811448	1.00[AMR][1000 genomes]
rs73813208	1.00[AMR][1000 genomes]
rs73813209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813213	1.00[AMR][1000 genomes]
rs73813215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7735436	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
2	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
5	chr5:179744000-179766600	Weak transcription	Gastric	stomach
6	chr5:179746000-179760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
8	chr5:179752200-179759000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:179752400-179760800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:179752400-179760800	Weak transcription	Brain Substantia Nigra	brain
11	chr5:179755000-179759800	Enhancers	Placenta	Placenta
12	chr5:179755800-179760800	Weak transcription	Lung	lung
13	chr5:179756000-179760800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:179756200-179761000	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:179756200-179761600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:179756400-179760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:179756800-179759200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:179757000-179759000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179757000-179759200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:179757000-179761000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
22	chr5:179757200-179759000	Enhancers	Adipose Nuclei	Adipose
23	chr5:179757200-179759000	Enhancers	HSMM	muscle
24	chr5:179757200-179761000	Weak transcription	Fetal Brain Female	brain
25	chr5:179757400-179759000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:179757400-179759000	Enhancers	Fetal Lung	lung
27	chr5:179757400-179759000	Flanking Active TSS	Hela-S3	cervix
28	chr5:179757400-179759000	Enhancers	HSMMtube	muscle
29	chr5:179757400-179759200	Enhancers	HUVEC	blood vessel
30	chr5:179757400-179759600	Genic enhancers	H1 Cell Line	embryonic stem cell
31	chr5:179757400-179759600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:179757400-179759600	Enhancers	Ovary	ovary
33	chr5:179757400-179759800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:179757600-179759000	Flanking Active TSS	A549	lung
35	chr5:179757800-179759000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:179757800-179759000	Enhancers	NHDF-Ad	bronchial
37	chr5:179757800-179759200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:179757800-179759600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:179757800-179760600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:179757800-179765600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:179758000-179759000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr5:179758000-179759000	Enhancers	NHLF	lung
43	chr5:179758000-179761000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:179758200-179759000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:179758200-179759000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:179758200-179759000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:179758200-179759000	Genic enhancers	Fetal Stomach	stomach
48	chr5:179758200-179759000	Flanking Active TSS	NH-A	brain
49	chr5:179758200-179759000	Flanking Active TSS	Osteobl	bone
50	chr5:179758200-179760400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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