Variant report

Variant	rs17553053
Chromosome Location	chr3:118960610-118960611
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	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	USF2	chr3:118960465-118960660	HepG2	liver:	n/a	n/a
4	CTCF	chr3:118960349-118960666	Gliobla	brain:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
5	CTCF	chr3:118960360-118960627	HepG2	liver:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
6	CTCF	chr3:118960383-118960636	Hela-S3	cervix:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
7	RAD21	chr3:118960265-118960672	GM12878	blood:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
8	SMC3	chr3:118960320-118960694	K562	blood:	n/a	chr3:118960503-118960517
9	ARID3A	chr3:118959577-118960661	HepG2	liver:	n/a	n/a
10	CTCF	chr3:118960460-118960610	GM12866	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
11	CTCF	chr3:118960326-118960610	HepG2	liver:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
12	CTCF	chr3:118960388-118960646	LNCaP	prostate:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
13	ARID3A	chr3:118960307-118960621	K562	blood:	n/a	n/a
14	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
15	MYC	chr3:118958908-118960675	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr3:118960460-118960610	K562	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
17	CTCF	chr3:118960460-118960610	GM12801	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
18	CTCF	chr3:118960352-118960615	A549	lung:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
19	FOXA1	chr3:118960327-118960708	T-47D	breast:	n/a	n/a
20	RAD21	chr3:118960278-118960672	HepG2	liver:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
21	MXI1	chr3:118959376-118960686	GM12878	blood:	n/a	n/a
22	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
23	MAX	chr3:118959041-118960696	NB4	blood:	n/a	n/a
24	ATF2	chr3:118960243-118960740	GM12878	blood:	n/a	n/a
25	MAFK	chr3:118960432-118960660	K562	blood:	n/a	n/a
26	ELF1	chr3:118960243-118960633	A549	lung:	n/a	n/a
27	SP1	chr3:118960177-118960748	A549	lung:	n/a	n/a
28	SMC3	chr3:118960290-118960716	GM12878	blood:	n/a	chr3:118960503-118960517
29	CTCF	chr3:118960011-118960773	HCT-116	colon:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
30	CTCF	chr3:118960316-118960699	A549	lung:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
31	EBF1	chr3:118960379-118960645	GM12878	blood:	n/a	n/a
32	CTCF	chr3:118960405-118960647	Kidney_OC	kidney:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
33	ZNF143	chr3:118959607-118960651	Hela-S3	cervix:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
34	CHD2	chr3:118960291-118960625	Hela-S3	cervix:	n/a	n/a
35	MAZ	chr3:118960429-118960666	HepG2	liver:	n/a	n/a
36	MAZ	chr3:118960342-118960636	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr3:118960162-118960721	ECC-1	luminal epithelium:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
38	FOXA1	chr3:118960325-118960708	HepG2	liver:	n/a	n/a
39	TBL1XR1	chr3:118960325-118960625	K562	blood:	n/a	n/a
40	CTCF	chr3:118960401-118960622	GM13976	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
41	FOXA2	chr3:118960358-118960735	A549	lung:	n/a	n/a
42	CTCF	chr3:118960374-118960646	MCF-7	breast:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
43	CTCF	chr3:118960339-118960665	GM12878	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
44	POLR2A	chr3:118959031-118960628	GM12878	blood:	n/a	n/a
45	EGR1	chr3:118959396-118960634	HCT-116	colon:	n/a	chr3:118959859-118959873 chr3:118959863-118959872 chr3:118959861-118959876
46	CTCF	chr3:118960253-118960612	H1-hESC	embryonic stem cell:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
47	CTCF	chr3:118960460-118960610	HCM	heart:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
48	CTCF	chr3:118960460-118960610	GM12873	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
49	CTCF	chr3:118960374-118960648	GM13977	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
50	ZNF143	chr3:118960326-118960693	H1-hESC	embryonic stem cell:	n/a	n/a

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
ENSG00000241155	Chromatin interaction
ENSG00000251012	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000144847	Chromatin interaction
ENSG00000163424	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11928941	1.00[ASN][1000 genomes]
rs3796355	1.00[EUR][1000 genomes]
rs6797796	1.00[EUR][1000 genomes]
rs72655912	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625545	1.00[EUR][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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118959800-118961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:118960000-118960800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:118960000-118960800	Enhancers	Liver	Liver
4	chr3:118960000-118960800	Enhancers	Stomach Mucosa	stomach
5	chr3:118960000-118960800	Flanking Active TSS	A549	lung
6	chr3:118960000-118962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:118960000-118962600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:118960000-118964400	Weak transcription	Esophagus	oesophagus
9	chr3:118960200-118960800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:118960200-118960800	Enhancers	K562	blood
11	chr3:118960200-118961000	Enhancers	Right Ventricle	heart
12	chr3:118960200-118964200	Weak transcription	Psoas Muscle	Psoas
13	chr3:118960200-118964600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:118960200-118964600	Weak transcription	Right Atrium	heart
15	chr3:118960200-118964800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:118960400-118960800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr3:118960400-118960800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:118960400-118960800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:118960400-118960800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:118960400-118960800	Enhancers	Hela-S3	cervix
21	chr3:118960400-118960800	Enhancers	HepG2	liver
22	chr3:118960400-118964400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:118960400-118966200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:118960600-118960800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:118960600-118964400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:118960600-118964600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:118960600-118964800	Weak transcription	Adipose Nuclei	Adipose
28	chr3:118960600-118964800	Weak transcription	Placenta	Placenta

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