Variant report

Variant	rs56325540
Chromosome Location	chr5:179759316-179759317
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	CTCF	chr5:179759288-179759580	IMR90	lung:	n/a	n/a
2	HDAC2	chr5:179758988-179759367	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr5:179758860-179759434	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr5:179759195-179759581	A549	lung:	n/a	n/a
5	CTCF	chr5:179759260-179759410	NHDF-neo	bronchial:	n/a	n/a
6	TEAD4	chr5:179758906-179759387	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr5:179758769-179759532	ECC-1	luminal epithelium:	n/a	chr5:179759178-179759194
8	CTCF	chr5:179759280-179759430	SAEC	small airway:	n/a	n/a
9	RAD21	chr5:179758651-179759561	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr5:179758560-179759353	H1-hESC	embryonic stem cell:	n/a	chr5:179759178-179759194
11	CTCF	chr5:179759280-179759430	NHDF-neo	bronchial:	n/a	n/a
12	CTCF	chr5:179759300-179759450	HMEC	breast:	n/a	n/a
13	CTCF	chr5:179759276-179759609	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr5:179759036-179759447	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr5:179759300-179759450	MCF-7	breast:	n/a	n/a
16	CTCF	chr5:179759271-179759592	HepG2	liver:	n/a	n/a
17	CTCF	chr5:179759300-179759450	BE2_C	brain:	n/a	n/a
18	CTCF	chr5:179759300-179759450	A549	lung:	n/a	n/a
19	CTCF	chr5:179759087-179759650	MCF-7	breast:	n/a	n/a
20	CTCF	chr5:179759280-179759430	HFF-Myc	foreskin:	n/a	n/a
21	CTCF	chr5:179759300-179759450	HMF	breast:	n/a	n/a
22	MAX	chr5:179758911-179759402	ECC-1	luminal epithelium:	n/a	chr5:179759234-179759244
23	TEAD4	chr5:179758559-179759423	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:179759300-179759450	NHLF	lung:	n/a	n/a
25	CTCF	chr5:179759260-179759410	HAc	cerebellar:	n/a	n/a
26	CTCF	chr5:179759280-179759430	AG04450	lung:	n/a	n/a
27	POLR2A	chr5:179758548-179759465	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr5:179759300-179759450	HEK293	kidney:	n/a	n/a
29	CTCF	chr5:179759300-179759450	HPF	lung:	n/a	n/a
30	RAD21	chr5:179759295-179759553	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr5:179759300-179759450	BJ	skin:	n/a	n/a
32	RAD21	chr5:179759281-179759508	H1-hESC	embryonic stem cell:	n/a	n/a
33	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
34	CTCF	chr5:179759242-179759541	A549	lung:	n/a	n/a
35	CTCF	chr5:179759316-179759548	K562	blood:	n/a	n/a
36	MAX	chr5:179758915-179759406	H1-hESC	embryonic stem cell:	n/a	chr5:179759234-179759244
37	SIN3A	chr5:179758601-179759373	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr5:179759300-179759450	HCFaa	heart:	n/a	n/a
39	CTCF	chr5:179759280-179759430	HCT-116	colon:	n/a	n/a
40	TEAD4	chr5:179758757-179759386	ECC-1	luminal epithelium:	n/a	n/a
41	NFIC	chr5:179758628-179759388	ECC-1	luminal epithelium:	n/a	n/a
42	CTCF	chr5:179759300-179759450	SAEC	small airway:	n/a	n/a
43	ZNF143	chr5:179758757-179759481	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr5:179759300-179759450	AG09309	skin:	n/a	n/a
45	MAX	chr5:179757503-179759416	A549	lung:	n/a	chr5:179759234-179759244
46	E2F6	chr5:179758850-179759401	H1-hESC	embryonic stem cell:	n/a	chr5:179759241-179759250
47	MAX	chr5:179758937-179759408	H1-hESC	embryonic stem cell:	n/a	chr5:179759234-179759244
48	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
49	CTCF	chr5:179759300-179759450	GM12864	blood:	n/a	n/a
50	SMC3	chr5:179759268-179759501	Hela-S3	cervix:	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	chr5:179758118..179760214-chr5:179779421..179781494,2	MCF-7	breast:
4	chr5:179743533..179745138-chr5:179758966..179761002,2	K562	blood:

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

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs73343405	1.00[AMR][1000 genomes]
rs73343419	1.00[AMR][1000 genomes]
rs73355930	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:74 , 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	chr5:179752400-179760800	Weak transcription	Brain Germinal Matrix	brain
9	chr5:179752400-179760800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:179755000-179759800	Enhancers	Placenta	Placenta
11	chr5:179755800-179760800	Weak transcription	Lung	lung
12	chr5:179756000-179760800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179756200-179761000	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:179756200-179761600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:179756400-179760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:179757000-179761000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
18	chr5:179757200-179761000	Weak transcription	Fetal Brain Female	brain
19	chr5:179757400-179759600	Genic enhancers	H1 Cell Line	embryonic stem cell
20	chr5:179757400-179759600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:179757400-179759600	Enhancers	Ovary	ovary
22	chr5:179757400-179759800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:179757800-179759600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:179757800-179760600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:179757800-179765600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:179758000-179761000	Weak transcription	Brain Angular Gyrus	brain
27	chr5:179758200-179760400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:179758200-179760600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:179758400-179760800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:179758600-179761000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:179758600-179761400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:179758800-179760000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:179758800-179760800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:179758800-179761000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:179759000-179759400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:179759000-179759600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:179759000-179759600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:179759000-179759600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:179759000-179759600	Enhancers	Fetal Stomach	stomach
40	chr5:179759000-179759800	Weak transcription	HSMM	muscle
41	chr5:179759000-179760000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:179759000-179760400	Weak transcription	NHDF-Ad	bronchial
43	chr5:179759000-179760600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:179759000-179760600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:179759000-179760600	Weak transcription	Adipose Nuclei	Adipose
46	chr5:179759000-179760600	Weak transcription	Brain Anterior Caudate	brain
47	chr5:179759000-179760600	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:179759000-179760600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr5:179759000-179760600	Enhancers	Hela-S3	cervix
50	chr5:179759000-179760800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links