Variant report

Variant	rs28729473
Chromosome Location	chr4:74733611-74733612
allele	C/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	STAT3	chr4:74733485-74733814	MCF10A-Er-Src	breast:	n/a	chr4:74733540-74733547
2	RAD21	chr4:74733479-74733997	HCT-116	colon:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
3	MYC	chr4:74733520-74734278	MCF10A-Er-Src	breast:	n/a	chr4:74734155-74734166
4	CTCF	chr4:74733560-74733710	GM12865	blood:	n/a	n/a
5	CTCF	chr4:74733580-74733730	HRE	kidney:	n/a	n/a
6	CTCF	chr4:74733611-74733785	LNCaP	prostate:	n/a	n/a
7	RAD21	chr4:74733501-74733917	A549	lung:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
8	CTCF	chr4:74733580-74733730	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr4:74733560-74733710	HRPEpiC	eye:	n/a	n/a
10	RAD21	chr4:74733535-74733922	ECC-1	luminal epithelium:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
11	CTCF	chr4:74733572-74733878	K562	blood:	n/a	n/a
12	CTCF	chr4:74733600-74733750	Caco-2	colon:	n/a	n/a
13	CTCF	chr4:74733600-74733750	HCT-116	colon:	n/a	n/a
14	CTCF	chr4:74733597-74733787	LNCaP	prostate:	n/a	n/a
15	FOSL2	chr4:74733508-74733922	A549	lung:	n/a	chr4:74733839-74733850
16	RAD21	chr4:74733562-74733924	H1-hESC	embryonic stem cell:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
17	FOS	chr4:74733486-74733811	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr4:74733462-74733831	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr4:74733484-74733892	MCF10A-Er-Src	breast:	n/a	chr4:74733839-74733850
20	RAD21	chr4:74733562-74733858	Hela-S3	cervix:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
21	CTCF	chr4:74733534-74733818	A549	lung:	n/a	n/a
22	CTCF	chr4:74733442-74734003	HCT-116	colon:	n/a	n/a
23	RAD21	chr4:74733584-74733787	HepG2	liver:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
24	CTCF	chr4:74733573-74733839	NHEK	skin:	n/a	n/a
25	CTCF	chr4:74733600-74733750	HRE	kidney:	n/a	n/a
26	CTCF	chr4:74733585-74733849	K562	blood:	n/a	n/a
27	RAD21	chr4:74733565-74733780	K562	blood:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
28	RAD21	chr4:74733522-74733876	HepG2	liver:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
29	TCF12	chr4:74733476-74733950	A549	lung:	n/a	n/a
30	CTCF	chr4:74733541-74733849	GM12878	blood:	n/a	n/a
31	SMC3	chr4:74733588-74733855	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr4:74733580-74733730	RPTEC	kidney:	n/a	n/a
33	CTCF	chr4:74733592-74733788	Pancreas_OC	pancreas:	n/a	n/a
34	CTCF	chr4:74733558-74734027	A549	lung:	n/a	n/a
35	STAT3	chr4:74733485-74733831	MCF10A-Er-Src	breast:	n/a	chr4:74733540-74733547
36	CTCF	chr4:74733580-74733730	MCF-7	breast:	n/a	n/a
37	CTCF	chr4:74733600-74733750	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr4:74733554-74733868	H1-hESC	embryonic stem cell:	n/a	n/a
39	STAT3	chr4:74733508-74733813	MCF10A-Er-Src	breast:	n/a	chr4:74733540-74733547
40	CTCF	chr4:74733604-74733791	Hela-S3	cervix:	n/a	n/a
41	RAD21	chr4:74733558-74733888	H1-hESC	embryonic stem cell:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
42	CTCF	chr4:74733491-74733842	A549	lung:	n/a	n/a
43	RAD21	chr4:74733588-74733931	A549	lung:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
44	RAD21	chr4:74733515-74733913	H1-hESC	embryonic stem cell:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
45	FOXA1	chr4:74733598-74733782	T-47D	breast:	n/a	n/a
46	MYC	chr4:74733537-74734575	MCF10A-Er-Src	breast:	n/a	chr4:74734155-74734166
47	RAD21	chr4:74733485-74734038	HCT-116	colon:	n/a	chr4:74733695-74733705 chr4:74733695-74733707
48	FOS	chr4:74733464-74733824	MCF10A-Er-Src	breast:	n/a	n/a
49	CTCF	chr4:74733574-74733771	H1-hESC	embryonic stem cell:	n/a	n/a
50	STAT3	chr4:74733608-74734460	MCF10A-Er-Src	breast:	n/a	chr4:74734034-74734041 chr4:74733971-74733979

No.	Distal block	Cell Line	Cell type
1	chr4:74719674..74726110-chr4:74728599..74734688,9	K562	blood:
2	chr4:74710377..74712305-chr4:74732116..74734240,2	K562	blood:
3	chr4:74710805..74713801-chr4:74732116..74734607,2	K562	blood:

Variant related genes	Relation type
CXCL1	TF binding region
ENSG00000250550	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28530514	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61709120	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73828896	0.97[ASN][1000 genomes]
rs73830317	0.87[ASN][1000 genomes]
rs73830318	0.87[ASN][1000 genomes]
rs73830323	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74726000-74734200	Weak transcription	HSMM	muscle
2	chr4:74726400-74733800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:74728600-74734200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:74728800-74734000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:74731400-74734200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:74731600-74734000	Enhancers	NHEK	skin
7	chr4:74731600-74734400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:74732000-74733800	Enhancers	A549	lung
9	chr4:74732000-74734400	Enhancers	HMEC	breast
10	chr4:74732400-74733800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:74732400-74734000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:74732400-74734200	Weak transcription	Liver	Liver
13	chr4:74732600-74734200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:74732800-74734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:74733000-74735000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:74733200-74734400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:74733600-74733800	Enhancers	Pancreas	Pancrea
18	chr4:74733600-74734000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr4:74733600-74734000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:74733600-74734000	Enhancers	Fetal Intestine Large	intestine
21	chr4:74733600-74734000	Enhancers	HUVEC	blood vessel
22	chr4:74733600-74734200	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr4:74733600-74734400	Enhancers	Thymus	Thymus
24	chr4:74733600-74734400	Enhancers	NHDF-Ad	bronchial
25	chr4:74733600-74734600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:74733600-74734600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr4:74733600-74734600	Enhancers	Placenta	Placenta
28	chr4:74733600-74734800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr4:74733600-74738800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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