Variant report

Variant	rs7655442
Chromosome Location	chr4:54458165-54458166
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	chr4:54457417-54458202	MCF-7	breast:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
2	EP300	chr4:54457550-54458412	K562	blood:	n/a	n/a
3	EP300	chr4:54457533-54458310	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr4:54457465-54458225	ECC-1	luminal epithelium:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
5	SIN3A	chr4:54457160-54458179	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr4:54457201-54458293	MCF-7	breast:	n/a	n/a
7	USF1	chr4:54457486-54458185	ECC-1	luminal epithelium:	n/a	n/a
8	JUN	chr4:54457166-54459864	K562	blood:	n/a	chr4:54457728-54457737 chr4:54459353-54459364
9	MAFK	chr4:54458144-54458668	K562	blood:	n/a	chr4:54458209-54458223 chr4:54458206-54458221 chr4:54458210-54458221 chr4:54458211-54458222 chr4:54458210-54458221
10	MAX	chr4:54457458-54458266	ECC-1	luminal epithelium:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
11	TEAD4	chr4:54457499-54458171	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr4:54457379-54458165	ECC-1	luminal epithelium:	n/a	n/a
13	MAFK	chr4:54458064-54458367	HepG2	liver:	n/a	chr4:54458209-54458223 chr4:54458206-54458221 chr4:54458210-54458221 chr4:54458211-54458222 chr4:54458210-54458221
14	RAD21	chr4:54457476-54458200	HCT-116	colon:	n/a	n/a
15	STAT3	chr4:54458121-54458567	MCF10A-Er-Src	breast:	n/a	chr4:54458286-54458294 chr4:54458444-54458452 chr4:54458253-54458265
16	MAX	chr4:54457463-54458175	MCF-7	breast:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
17	NFIC	chr4:54457552-54458191	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr4:54457309-54458234	HCT-116	colon:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53577014..53579334-chr4:54455969..54458582,2	K562	blood:
2	chr4:54441539..54444052-chr4:54456319..54458612,3	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region
LNX1-AS2	TF binding region
ENSG00000264585	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000173966	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs907509	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9312642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs979006	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879014	chr4:54451246-54461548	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54452600-54458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:54452600-54459600	Enhancers	HepG2	liver
3	chr4:54452800-54458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:54452800-54459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:54453000-54458800	Weak transcription	Small Intestine	intestine
6	chr4:54453200-54459200	Weak transcription	Osteobl	bone
7	chr4:54454200-54458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:54454600-54459000	Enhancers	Fetal Muscle Leg	muscle
9	chr4:54454800-54459000	Weak transcription	Aorta	Aorta
10	chr4:54455400-54458400	Weak transcription	Left Ventricle	heart
11	chr4:54455800-54458200	Weak transcription	Fetal Heart	heart
12	chr4:54455800-54459000	Enhancers	Adipose Nuclei	Adipose
13	chr4:54456000-54458200	Active TSS	Duodenum Mucosa	Duodenum
14	chr4:54456000-54458200	Active TSS	Pancreas	Pancrea
15	chr4:54456000-54460000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:54456200-54458200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr4:54456200-54458600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:54456400-54458200	Active TSS	Stomach Mucosa	stomach
19	chr4:54456800-54458600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:54456800-54459000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr4:54457000-54458200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr4:54457000-54458400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr4:54457000-54459000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr4:54457000-54459200	Enhancers	Fetal Lung	lung
25	chr4:54457200-54460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:54457400-54458200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr4:54457400-54458400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:54457400-54459000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr4:54457400-54459000	Enhancers	Fetal Muscle Trunk	muscle
30	chr4:54457400-54459000	Enhancers	Right Atrium	heart
31	chr4:54457400-54459600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:54457400-54459800	Flanking Active TSS	NHEK	skin
33	chr4:54457600-54458200	Flanking Active TSS	Liver	Liver
34	chr4:54457600-54458200	Weak transcription	Gastric	stomach
35	chr4:54457600-54458200	Flanking Active TSS	HMEC	breast
36	chr4:54457600-54458400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr4:54457600-54458400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:54457600-54458600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:54457600-54458800	Enhancers	Right Ventricle	heart
40	chr4:54457600-54459000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:54457600-54459000	Weak transcription	Colonic Mucosa	Colon
42	chr4:54457600-54459000	Flanking Active TSS	K562	blood
43	chr4:54457600-54459000	Enhancers	NH-A	brain
44	chr4:54457600-54459800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:54457600-54460200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:54457600-54464400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:54457800-54458200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr4:54457800-54458200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr4:54457800-54458200	Flanking Active TSS	Placenta	Placenta
50	chr4:54457800-54458600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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