Variant report

Variant	rs72655916
Chromosome Location	chr3:118960592-118960593
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	chr3:118960363-118960637	Pancreas_OC	pancreas:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
2	FOXA1	chr3:118960340-118960752	HepG2	liver:	n/a	n/a
3	CTCF	chr3:118960396-118960606	MCF-7	breast:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
4	USF2	chr3:118960465-118960660	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:118960387-118960597	K562	blood:	n/a	n/a
6	CTCF	chr3:118960349-118960666	Gliobla	brain:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
7	CTCF	chr3:118960360-118960627	HepG2	liver:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
8	CTCF	chr3:118960383-118960636	Hela-S3	cervix:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
9	RAD21	chr3:118960265-118960672	GM12878	blood:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
10	SMC3	chr3:118960320-118960694	K562	blood:	n/a	chr3:118960503-118960517
11	ARID3A	chr3:118959577-118960661	HepG2	liver:	n/a	n/a
12	CTCF	chr3:118960460-118960610	GM12866	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
13	CTCF	chr3:118960326-118960610	HepG2	liver:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
14	CTCF	chr3:118960388-118960646	LNCaP	prostate:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
15	ARID3A	chr3:118960307-118960621	K562	blood:	n/a	n/a
16	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
17	MYC	chr3:118958908-118960675	MCF10A-Er-Src	breast:	n/a	n/a
18	CTCF	chr3:118960460-118960610	K562	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
19	CTCF	chr3:118960460-118960610	GM12801	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
20	CTCF	chr3:118960352-118960615	A549	lung:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
21	FOXA1	chr3:118960327-118960708	T-47D	breast:	n/a	n/a
22	RAD21	chr3:118960278-118960672	HepG2	liver:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
23	MXI1	chr3:118959376-118960686	GM12878	blood:	n/a	n/a
24	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
25	CTCF	chr3:118960417-118960593	H1-hESC	embryonic stem cell:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
26	MAX	chr3:118959041-118960696	NB4	blood:	n/a	n/a
27	ATF2	chr3:118960243-118960740	GM12878	blood:	n/a	n/a
28	MAFK	chr3:118960432-118960660	K562	blood:	n/a	n/a
29	ELF1	chr3:118960243-118960633	A549	lung:	n/a	n/a
30	SP1	chr3:118960177-118960748	A549	lung:	n/a	n/a
31	SMC3	chr3:118960290-118960716	GM12878	blood:	n/a	chr3:118960503-118960517
32	CTCF	chr3:118960011-118960773	HCT-116	colon:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
33	CTCF	chr3:118960316-118960699	A549	lung:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
34	EBF1	chr3:118960379-118960645	GM12878	blood:	n/a	n/a
35	CTCF	chr3:118960405-118960647	Kidney_OC	kidney:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
36	ZNF143	chr3:118959607-118960651	Hela-S3	cervix:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
37	CHD2	chr3:118960291-118960625	Hela-S3	cervix:	n/a	n/a
38	MAZ	chr3:118960429-118960666	HepG2	liver:	n/a	n/a
39	MAZ	chr3:118960342-118960636	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr3:118960162-118960721	ECC-1	luminal epithelium:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
41	FOXA1	chr3:118960325-118960708	HepG2	liver:	n/a	n/a
42	TBL1XR1	chr3:118960325-118960625	K562	blood:	n/a	n/a
43	CTCF	chr3:118960401-118960622	GM13976	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
44	FOXA2	chr3:118960358-118960735	A549	lung:	n/a	n/a
45	CTCF	chr3:118960374-118960646	MCF-7	breast:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
46	CTCF	chr3:118960339-118960665	GM12878	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
47	POLR2A	chr3:118959031-118960628	GM12878	blood:	n/a	n/a
48	EGR1	chr3:118959396-118960634	HCT-116	colon:	n/a	chr3:118959859-118959873 chr3:118959863-118959872 chr3:118959861-118959876
49	CTCF	chr3:118960253-118960612	H1-hESC	embryonic stem cell:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
50	RAD21	chr3:118960356-118960592	K562	blood:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517

No.	Distal block	Cell Line	Cell type
1	chr3:118603243..118603893-chr3:118960392..118961051,3	MCF-7	breast:
2	chr3:118866560..118867342-chr3:118960209..118960801,2	MCF-7	breast:
3	chr3:118864340..118865141-chr3:118960015..118960938,2	MCF-7	breast:
4	chr3:118865607..118868236-chr3:118959699..118961355,2	K562	blood:
5	chr3:118864376..118864922-chr3:118960063..118960873,2	K562	blood:
6	chr3:118948357..118951865-chr3:118958522..118961643,4	MCF-7	breast:
7	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:
8	chr3:118960420..118962594-chr3:119040439..119042799,2	MCF-7	breast:
9	chr3:118863219..118864917-chr3:118959824..118960983,11	MCF-7	breast:
10	chr3:118948409..118952425-chr3:118955700..118962526,10	K562	blood:
11	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:

Variant related genes	Relation type
B4GALT4	TF binding region
ENSG00000121578	Chromatin interaction
ENSG00000251012	Chromatin interaction
ENSG00000144847	Chromatin interaction
ENSG00000163424	Chromatin interaction
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6762910	1.00[AFR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405597	chr3:118958287-118960835	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118959200-118960600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:118959800-118960600	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:118959800-118960600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr3:118959800-118960600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:118959800-118961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:118960000-118960600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:118960000-118960600	Enhancers	Fetal Stomach	stomach
8	chr3:118960000-118960600	Flanking Active TSS	Rectal Smooth Muscle	rectum
9	chr3:118960000-118960600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:118960000-118960800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:118960000-118960800	Enhancers	Liver	Liver
12	chr3:118960000-118960800	Enhancers	Stomach Mucosa	stomach
13	chr3:118960000-118960800	Flanking Active TSS	A549	lung
14	chr3:118960000-118962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:118960000-118962600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:118960000-118964400	Weak transcription	Esophagus	oesophagus
17	chr3:118960200-118960600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:118960200-118960600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr3:118960200-118960600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:118960200-118960600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:118960200-118960600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:118960200-118960600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:118960200-118960600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:118960200-118960600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:118960200-118960600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:118960200-118960600	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:118960200-118960600	Enhancers	Brain Hippocampus Middle	brain
28	chr3:118960200-118960600	Enhancers	Fetal Muscle Leg	muscle
29	chr3:118960200-118960600	Enhancers	Placenta	Placenta
30	chr3:118960200-118960600	Enhancers	Fetal Thymus	thymus
31	chr3:118960200-118960600	Enhancers	Ovary	ovary
32	chr3:118960200-118960600	Enhancers	Thymus	Thymus
33	chr3:118960200-118960600	Enhancers	Dnd41	blood
34	chr3:118960200-118960600	Enhancers	HMEC	breast
35	chr3:118960200-118960600	Enhancers	HSMMtube	muscle
36	chr3:118960200-118960600	Enhancers	HUVEC	blood vessel
37	chr3:118960200-118960600	Enhancers	NHLF	lung
38	chr3:118960200-118960800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:118960200-118960800	Enhancers	K562	blood
40	chr3:118960200-118961000	Enhancers	Right Ventricle	heart
41	chr3:118960200-118964200	Weak transcription	Psoas Muscle	Psoas
42	chr3:118960200-118964600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:118960200-118964600	Weak transcription	Right Atrium	heart
44	chr3:118960200-118964800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:118960400-118960600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr3:118960400-118960600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:118960400-118960600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:118960400-118960600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:118960400-118960600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr3:118960400-118960600	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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