Variant report

Variant	rs552381378
Chromosome Location	chr3:24535523-24535524
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	chr3:24535467-24537699	A549	lung:	n/a	chr3:24536750-24536759 chr3:24535554-24535567 chr3:24536379-24536392 chr3:24536385-24536398
2	POLR2A	chr3:24535426-24536677	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr3:24535385-24537221	K562	blood:	n/a	n/a
4	HA-E2F1	chr3:24535299-24537654	MCF-7	breast:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
5	HEY1	chr3:24535449-24537529	K562	blood:	n/a	chr3:24536750-24536765 chr3:24536479-24536494 chr3:24536491-24536506 chr3:24536707-24536722 chr3:24536792-24536807
6	MYBL2	chr3:24535420-24535985	HepG2	liver:	n/a	n/a
7	ZEB1	chr3:24535519-24537509	HepG2	liver:	n/a	chr3:24536969-24536980
8	KAP1	chr3:24535378-24535973	HEK293	kidney:	n/a	chr3:24535568-24535576
9	NFIC	chr3:24535339-24536486	ECC-1	luminal epithelium:	n/a	n/a
10	SP1	chr3:24535373-24536078	A549	lung:	n/a	n/a
11	MAX	chr3:24535349-24537594	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
12	MXI1	chr3:24535442-24537411	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:24535466-24537678	K562	blood:	n/a	n/a
14	EP300	chr3:24535384-24537629	ECC-1	luminal epithelium:	n/a	chr3:24536788-24536804 chr3:24536792-24536808 chr3:24536879-24536895 chr3:24536719-24536728 chr3:24536794-24536803 chr3:24536386-24536402
15	MAZ	chr3:24535500-24537843	HepG2	liver:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
16	RFX5	chr3:24535466-24536285	HepG2	liver:	n/a	chr3:24535575-24535590
17	POLR2A	chr3:24535405-24537667	HepG2	liver:	n/a	n/a
18	SMARCB1	chr3:24535448-24537477	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr3:24535361-24536593	HepG2	liver:	n/a	n/a
20	NR2F2	chr3:24535202-24535849	K562	blood:	n/a	n/a
21	E2F6	chr3:24535505-24537406	K562	blood:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
22	HDAC2	chr3:24535444-24535972	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr3:24535393-24537604	ECC-1	luminal epithelium:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
24	SMARCC1	chr3:24535422-24537518	Hela-S3	cervix:	n/a	n/a
25	TAL1	chr3:24535417-24537447	K562	blood:	n/a	chr3:24537308-24537323 chr3:24537308-24537323 chr3:24537308-24537323 chr3:24537309-24537320
26	POLR2A	chr3:24535504-24537653	K562	blood:	n/a	n/a
27	E2F4	chr3:24535387-24537486	K562	blood:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
28	POLR2A	chr3:24535410-24537534	K562	blood:	n/a	n/a
29	SIN3A	chr3:24535427-24537395	H1-hESC	embryonic stem cell:	n/a	chr3:24536206-24536219 chr3:24536886-24536895 chr3:24536608-24536617
30	MYC	chr3:24535387-24537606	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
31	MYBL2	chr3:24535516-24536102	HepG2	liver:	n/a	n/a
32	CTCF	chr3:24535480-24535630	HMEC	breast:	n/a	chr3:24535554-24535567
33	CTCF	chr3:24535440-24535590	HEK293	kidney:	n/a	chr3:24535554-24535567
34	RAD21	chr3:24535513-24535716	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr3:24535420-24535570	AG09319	gingival:	n/a	chr3:24535554-24535567
36	ZNF263	chr3:24535354-24537587	HEK293-T-REx	kidney:	n/a	chr3:24537226-24537235 chr3:24536385-24536394 chr3:24536129-24536138 chr3:24537115-24537136
37	UBTF	chr3:24535396-24537447	K562	blood:	n/a	n/a
38	SMC3	chr3:24535424-24535837	HepG2	liver:	n/a	chr3:24535557-24535567
39	RCOR1	chr3:24535262-24537500	K562	blood:	n/a	n/a
40	TBP	chr3:24535428-24536589	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:24535459-24537514	HepG2	liver:	n/a	n/a
42	CTCF	chr3:24535380-24535530	NHDF-neo	bronchial:	n/a	n/a
43	TBL1XR1	chr3:24535407-24535906	K562	blood:	n/a	n/a
44	MBD4	chr3:24535516-24535972	HepG2	liver:	n/a	n/a
45	CTCF	chr3:24535480-24535630	HRE	kidney:	n/a	chr3:24535554-24535567
46	POLR2A	chr3:24535265-24536182	H1-neurons	neurons:	n/a	n/a
47	CEBPB	chr3:24535235-24536086	K562	blood:	n/a	n/a
48	MAX	chr3:24535335-24537639	HepG2	liver:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
49	CTBP2	chr3:24535443-24537316	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:24535470-24537527	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:57466622..57469005-chr3:24535228..24537121,2	MCF-7	breast:
2	chr3:23846193..23848940-chr3:24535065..24537255,2	K562	blood:
3	chr3:24535191..24540424-chr3:24558354..24564929,10	K562	blood:
4	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
5	chr3:24497472..24501858-chr3:24535149..24538807,5	MCF-7	breast:
6	chr3:24534533..24538643-chr3:24561395..24564731,10	MCF-7	breast:
7	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:

Variant related genes	Relation type
THRB-AS1	TF binding region
ENSG00000224822	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000087460	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000265028	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3341544	chr3:24535373-24538321	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24533600-24535600	Active TSS	Fetal Intestine Small	intestine
2	chr3:24533600-24537200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:24533600-24537800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:24533800-24537000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr3:24533800-24537400	Active TSS	Brain Angular Gyrus	brain
6	chr3:24534000-24537000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr3:24534000-24537000	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:24534200-24537000	Active TSS	Liver	Liver
9	chr3:24534400-24537000	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:24534400-24538200	Active TSS	Aorta	Aorta
11	chr3:24534600-24535800	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr3:24534600-24537200	Active TSS	Psoas Muscle	Psoas
13	chr3:24534600-24537400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr3:24534600-24537600	Active TSS	Brain Anterior Caudate	brain
15	chr3:24534600-24537600	Active TSS	Brain Cingulate Gyrus	brain
16	chr3:24534800-24536400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:24534800-24537200	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr3:24534800-24537400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:24534800-24537400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:24534800-24537400	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:24534800-24537400	Active TSS	Stomach Mucosa	stomach
22	chr3:24535000-24535600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:24535000-24535600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:24535000-24536000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:24535000-24536600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:24535000-24537200	Active TSS	Brain Hippocampus Middle	brain
27	chr3:24535000-24537400	Active TSS	Colon Smooth Muscle	Colon
28	chr3:24535000-24537600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:24535000-24537600	Active TSS	Right Ventricle	heart
30	chr3:24535200-24535600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:24535200-24535600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr3:24535200-24535600	Flanking Bivalent TSS/Enh	A549	lung
33	chr3:24535200-24535600	Flanking Active TSS	K562	blood
34	chr3:24535200-24535800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr3:24535200-24535800	Bivalent/Poised TSS	HSMM	muscle
36	chr3:24535200-24536000	Bivalent/Poised TSS	NHLF	lung
37	chr3:24535200-24536400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:24535200-24536400	Bivalent/Poised TSS	HepG2	liver
39	chr3:24535200-24536600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
40	chr3:24535200-24536800	Active TSS	HMEC	breast
41	chr3:24535200-24537000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:24535200-24537000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:24535200-24537200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:24535200-24537200	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:24535200-24537200	Active TSS	Right Atrium	heart
46	chr3:24535200-24537200	Active TSS	HSMMtube	muscle
47	chr3:24535200-24537400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:24535200-24537400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:24535200-24537400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr3:24535200-24537400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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