Variant report

Variant	rs57941453
Chromosome Location	chr3:134513719-134513720
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	TBL1XR1	chr3:134513666-134514438	GM12878	blood:	n/a	n/a
2	CTCF	chr3:134513711-134514123	K562	blood:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
3	YY1	chr3:134513714-134514211	GM12878	blood:	n/a	n/a
4	RAD21	chr3:134513603-134514207	A549	lung:	n/a	chr3:134513885-134513904
5	MAZ	chr3:134513695-134514045	K562	blood:	n/a	n/a
6	RAD21	chr3:134513573-134514292	HCT-116	colon:	n/a	chr3:134513885-134513904
7	RAD21	chr3:134513422-134514439	SK-N-SH	brain:	n/a	chr3:134513885-134513904
8	REST	chr3:134513559-134517109	H1-neurons	neurons:	n/a	chr3:134515459-134515469 chr3:134513816-134513824 chr3:134514415-134514428 chr3:134515274-134515284 chr3:134515272-134515292 chr3:134514323-134514336 chr3:134514680-134514693 chr3:134514418-134514436 chr3:134515452-134515465
9	RAD21	chr3:134513705-134514141	SK-N-SH_RA	brain:	n/a	chr3:134513885-134513904
10	ELF1	chr3:134513694-134514338	MCF-7	breast:	n/a	n/a
11	SP1	chr3:134513672-134514405	GM12878	blood:	n/a	chr3:134514316-134514326 chr3:134514082-134514096 chr3:134513988-134514009 chr3:134514052-134514063
12	EGR1	chr3:134513694-134514571	MCF-7	breast:	n/a	chr3:134514320-134514329 chr3:134514269-134514283 chr3:134514318-134514331 chr3:134514319-134514329 chr3:134514317-134514331 chr3:134514315-134514329 chr3:134514319-134514330 chr3:134514319-134514329 chr3:134514317-134514332 chr3:134514312-134514325 chr3:134514313-134514335 chr3:134514318-134514331 chr3:134514319-134514330 chr3:134514318-134514331 chr3:134514319-134514328
13	POLR2A	chr3:134513627-134514412	GM12878	blood:	n/a	n/a
14	E2F6	chr3:134513703-134514394	H1-hESC	embryonic stem cell:	n/a	chr3:134514359-134514366 chr3:134514359-134514366 chr3:134514358-134514366 chr3:134513999-134514008 chr3:134514359-134514366
15	RAD21	chr3:134513514-134514277	HCT-116	colon:	n/a	chr3:134513885-134513904
16	SMC3	chr3:134513678-134514119	Hela-S3	cervix:	n/a	chr3:134513886-134513900 chr3:134513886-134513894
17	YY1	chr3:134513717-134514472	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr3:134513718-134514101	T-47D	breast:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
19	RAD21	chr3:134513692-134514168	ECC-1	luminal epithelium:	n/a	chr3:134513885-134513904
20	RUNX3	chr3:134513697-134514105	GM12878	blood:	n/a	n/a
21	ZNF143	chr3:134513713-134514521	GM12878	blood:	n/a	chr3:134514401-134514419 chr3:134514423-134514433
22	RAD21	chr3:134513544-134514221	MCF-7	breast:	n/a	chr3:134513885-134513904
23	CTCF	chr3:134513624-134514139	MCF-7	breast:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
24	RAD21	chr3:134513649-134514196	HepG2	liver:	n/a	chr3:134513885-134513904
25	RAD21	chr3:134513715-134514196	HepG2	liver:	n/a	chr3:134513885-134513904
26	SMC3	chr3:134513477-134514759	SK-N-SH	brain:	n/a	chr3:134514713-134514727 chr3:134513886-134513900 chr3:134513886-134513894
27	CTCF	chr3:134513695-134514022	A549	lung:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
28	CTCF	chr3:134513661-134514292	GM12878	blood:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
29	FOXM1	chr3:134513613-134514155	GM12878	blood:	n/a	n/a
30	TCF12	chr3:134513636-134514517	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr3:134513529-134514345	SK-N-SH	brain:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
32	CTCF	chr3:134513690-134514009	ECC-1	luminal epithelium:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
33	CTCF	chr3:134513577-134514244	HCT-116	colon:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
34	MAX	chr3:134513639-134514605	ECC-1	luminal epithelium:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
35	CHD1	chr3:134513715-134515047	GM12878	blood:	n/a	n/a
36	YY1	chr3:134513693-134514093	GM12878	blood:	n/a	n/a
37	HDAC2	chr3:134513683-134514480	MCF-7	breast:	n/a	n/a
38	FOXM1	chr3:134513667-134514338	MCF-7	breast:	n/a	n/a
39	MAX	chr3:134513667-134514532	H1-hESC	embryonic stem cell:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
40	RAD21	chr3:134513679-134514212	H1-hESC	embryonic stem cell:	n/a	chr3:134513885-134513904
41	POU2F2	chr3:134513638-134514525	GM12878	blood:	n/a	n/a
42	CTCF	chr3:134513679-134514368	A549	lung:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
43	MAX	chr3:134513691-134514379	A549	lung:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
44	MAX	chr3:134513687-134514554	H1-hESC	embryonic stem cell:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
45	CTCF	chr3:134513574-134514303	MCF-7	breast:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
46	RAD21	chr3:134513517-134515198	H1-hESC	embryonic stem cell:	n/a	chr3:134514713-134514727 chr3:134514709-134514728 chr3:134513885-134513904
47	CTCF	chr3:134513718-134513719	NHEK	skin:	n/a	n/a
48	RAD21	chr3:134513488-134514189	MCF-7	breast:	n/a	chr3:134513885-134513904
49	MAX	chr3:134513662-134514428	MCF-7	breast:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
50	SMC3	chr3:134513669-134514450	GM12878	blood:	n/a	chr3:134513886-134513900 chr3:134513886-134513894

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:134513690-134513740	Hela-S3	cervix:	n/a
2	chr3:134513690-134513740	HCM	heart:	n/a
3	chr3:134513690-134513740	BE2_C	brain:	n/a
4	chr3:134513690-134513740	HCF	heart:	n/a
5	chr3:134513690-134513740	MCF10A-Er-Src	breast:	n/a
6	chr3:134513690-134513740	LNCaP	prostate:	n/a
7	chr3:134513690-134513740	HCPEpiC	choroid plexus:	n/a
8	chr3:134513690-134513740	NT2-D1	testis:	n/a
9	chr3:134513690-134513740	NB4	blood:	n/a
10	chr3:134513690-134513740	AG04450	lung:	fetal
11	chr3:134513690-134513740	HNPCEpiC	eye:	n/a
12	chr3:134513690-134513740	U87	brain:	n/a
13	chr3:134513690-134513740	SKMC	muscle:	n/a
14	chr3:134513690-134513740	HRE	kidney:	n/a
15	chr3:134513690-134513740	ProgFib	skin:	n/a
16	chr3:134513690-134513740	CMK	blood:	n/a
17	chr3:134513690-134513740	SK-N-SH	brain:	n/a
18	chr3:134513690-134513740	AG09319	gingival:	n/a
19	chr3:134513690-134513740	Hepatocyte	liver:	n/a
20	chr3:134513690-134513740	AG09309	skin:	n/a
21	chr3:134513690-134513740	HMEC	breast:	n/a
22	chr3:134513690-134513740	T-47D	breast:	n/a
23	chr3:134513690-134513740	Jurkat	blood:	n/a
24	chr3:134513690-134513740	RPTEC	kidney:	n/a
25	chr3:134513690-134513740	A549	lung:	n/a
26	chr3:134513690-134513740	IMR90	lung:	fetal
27	chr3:134513690-134513740	AG04449	skin:	fetal
28	chr3:134513690-134513740	NH-A	brain:	n/a
29	chr3:134513690-134513740	MCF-7	breast:	n/a
30	chr3:134513690-134513740	HRCEpiC	kidney:	n/a
31	chr3:134513690-134513740	GM19239	blood:	n/a
32	chr3:134513690-134513740	GM06990	blood:	n/a
33	chr3:134513690-134513740	HEK293	kidney:	embryo
34	chr3:134513690-134513740	SAEC	small airway:	n/a
35	chr3:134513690-134513740	H1-hESC	embryonic stem cell:	embryo
36	chr3:134513690-134513740	HIPEpiC	eye:	n/a
37	chr3:134513690-134513740	BJ	skin:	n/a
38	chr3:134513690-134513740	Caco-2	colon:	n/a
39	chr3:134513690-134513740	HepG2	liver:	n/a
40	chr3:134513690-134513740	SK-N-SH_RA	brain:	n/a
41	chr3:134513690-134513740	HUVEC	blood vessel:	n/a
42	chr3:134513690-134513740	PFSK-1	brain:	n/a
43	chr3:134513690-134513740	AoSMC	blood vessel:	n/a
44	chr3:134513690-134513740	NHDF-neo	bronchial:	n/a
45	chr3:134513690-134513740	SK-N-MC	brain:	n/a
46	chr3:134513690-134513740	PANC-1	pancreas:	n/a
47	chr3:134513690-134513740	GM12891	blood:	n/a
48	chr3:134513690-134513740	HAEpiC	amniotic membrane:	n/a
49	chr3:134513690-134513740	HPAEpiC	pulmonary alveolar:	n/a
50	chr3:134513690-134513740	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134513497..134514031-chr3:134964955..134965488,2	MCF-7	breast:

Variant related genes	Relation type
EPHB1	TF binding region
EPHB1	CpG island

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs62272388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62272389	0.96[EUR][1000 genomes]
rs6439520	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6762299	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134511800-134513800	Weak transcription	Pancreas	Pancrea
2	chr3:134513000-134514000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:134513600-134513800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:134513600-134513800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr3:134513600-134513800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
6	chr3:134513600-134513800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:134513600-134513800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134513600-134513800	Enhancers	Adipose Nuclei	Adipose
9	chr3:134513600-134513800	Enhancers	Brain Angular Gyrus	brain
10	chr3:134513600-134513800	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:134513600-134513800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:134513600-134513800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:134513600-134513800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
14	chr3:134513600-134513800	Enhancers	Fetal Brain Female	brain
15	chr3:134513600-134513800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr3:134513600-134513800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:134513600-134514000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:134513600-134514000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
19	chr3:134513600-134514000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:134513600-134514000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr3:134513600-134514000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr3:134513600-134514000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:134513600-134514000	Enhancers	Liver	Liver
24	chr3:134513600-134514000	Enhancers	Brain Substantia Nigra	brain
25	chr3:134513600-134514000	Enhancers	Fetal Brain Male	brain
26	chr3:134513600-134514000	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr3:134513600-134514000	Bivalent Enhancer	Placenta	Placenta
28	chr3:134513600-134514000	Bivalent Enhancer	Fetal Stomach	stomach
29	chr3:134513600-134514000	Enhancers	Rectal Smooth Muscle	rectum
30	chr3:134513600-134514000	Active TSS	Spleen	Spleen
31	chr3:134513600-134514000	Enhancers	NH-A	brain
32	chr3:134513600-134514600	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr3:134513600-134514800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:134513600-134515000	Active TSS	GM12878-XiMat	blood
35	chr3:134513600-134515200	Active TSS	Brain Anterior Caudate	brain
36	chr3:134513600-134515600	Enhancers	Fetal Heart	heart
37	chr3:134513600-134516000	Bivalent/Poised TSS	HSMM	muscle

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