Variant report

Variant	rs574554241
Chromosome Location	chr5:178054077-178054078
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	ZNF384	chr5:178052770-178054463	K562	blood:	n/a	n/a
2	E2F6	chr5:178053942-178054425	K562	blood:	n/a	chr5:178053976-178053993 chr5:178054101-178054110 chr5:178054309-178054324 chr5:178053979-178053990 chr5:178054313-178054325 chr5:178053996-178054007
3	POLR2A	chr5:178053049-178054494	GM19099	blood:	n/a	n/a
4	YY1	chr5:178053290-178054169	GM12892	blood:	n/a	chr5:178054040-178054054 chr5:178054038-178054049 chr5:178054020-178054042 chr5:178054032-178054042 chr5:178054032-178054042 chr5:178054031-178054039
5	SMC3	chr5:178053135-178054427	Hela-S3	cervix:	n/a	chr5:178053454-178053464
6	RUNX3	chr5:178053104-178054187	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:178053171-178054584	Hela-S3	cervix:	n/a	n/a
8	BHLHE40	chr5:178052939-178054553	GM12878	blood:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054544-178054553
9	REST	chr5:178053410-178054201	HL-60	blood:	n/a	chr5:178053678-178053691
10	MYC	chr5:178052572-178054553	K562	blood:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054544-178054553 chr5:178054333-178054340
11	CEBPD	chr5:178053927-178054241	HepG2	liver:	n/a	n/a
12	RELA	chr5:178053313-178054213	GM12892	blood:	n/a	chr5:178053518-178053527 chr5:178053518-178053527
13	POLR2A	chr5:178053844-178054193	H1-hESC	embryonic stem cell:	n/a	n/a
14	HEY1	chr5:178053819-178054289	HepG2	liver:	n/a	n/a
15	ETS1	chr5:178053409-178054194	K562	blood:	n/a	n/a
16	POLR2A	chr5:178053380-178054426	GM10847	blood:	n/a	n/a
17	EP300	chr5:178053546-178054188	GM12878	blood:	n/a	n/a
18	TAF1	chr5:178053444-178054173	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:178053190-178054319	K562	blood:	n/a	n/a
20	USF1	chr5:178053909-178054316	A549	lung:	n/a	n/a
21	POLR2A	chr5:178053108-178054454	K562	blood:	n/a	n/a
22	RUNX3	chr5:178053311-178054207	GM12878	blood:	n/a	n/a
23	CTCF	chr5:178054032-178054177	Spleen_OC	spleen:	n/a	n/a
24	TAF1	chr5:178053165-178054219	H1-neurons	neurons:	n/a	n/a
25	TBL1XR1	chr5:178053274-178054539	GM12878	blood:	n/a	n/a
26	USF1	chr5:178053861-178054695	ECC-1	luminal epithelium:	n/a	chr5:178054543-178054552 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
27	POLR2A	chr5:178052968-178054585	H1-neurons	neurons:	n/a	n/a
28	CBX3	chr5:178053388-178054227	K562	blood:	n/a	n/a
29	EP300	chr5:178053514-178054218	GM12878	blood:	n/a	chr5:178054184-178054200
30	EP300	chr5:178053362-178054183	HepG2	liver:	n/a	n/a
31	TCF12	chr5:178053319-178054222	A549	lung:	n/a	chr5:178053550-178053558 chr5:178053881-178053888
32	POLR2A	chr5:178053265-178054482	ECC-1	luminal epithelium:	n/a	n/a
33	RFX5	chr5:178053426-178054196	GM12878	blood:	n/a	n/a
34	TAF1	chr5:178053349-178054328	ECC-1	luminal epithelium:	n/a	n/a
35	MXI1	chr5:178053869-178054200	K562	blood:	n/a	chr5:178054156-178054165
36	YY1	chr5:178053655-178054196	HepG2	liver:	n/a	chr5:178054040-178054054 chr5:178054038-178054049 chr5:178054020-178054042 chr5:178054032-178054042 chr5:178054032-178054042 chr5:178054031-178054039
37	TAF1	chr5:178053398-178054220	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr5:178053350-178054184	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr5:178053265-178054273	H1-hESC	embryonic stem cell:	n/a	n/a
40	CREB1	chr5:178053316-178054434	HepG2	liver:	n/a	n/a
41	NRF1	chr5:178053954-178054662	H1-hESC	embryonic stem cell:	n/a	chr5:178054189-178054203 chr5:178054228-178054237 chr5:178054099-178054110
42	TEAD4	chr5:178053783-178054178	K562	blood:	n/a	n/a
43	POLR2A	chr5:178052757-178054569	GM12878	blood:	n/a	n/a
44	EGR1	chr5:178053889-178054374	K562	blood:	n/a	chr5:178054228-178054238 chr5:178054215-178054228 chr5:178054341-178054354 chr5:178054224-178054234 chr5:178054228-178054243 chr5:178054220-178054230 chr5:178054078-178054092 chr5:178054221-178054231 chr5:178054101-178054110 chr5:178054219-178054229
45	POLR2A	chr5:178053394-178054441	MCF-7	breast:	n/a	n/a
46	CEBPB	chr5:178053918-178054322	HepG2	liver:	n/a	n/a
47	POLR2A	chr5:178052765-178054366	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:178052453-178054216	K562	blood:	n/a	n/a
49	POLR2A	chr5:178053144-178054193	GM12878	blood:	n/a	n/a
50	SP1	chr5:178053205-178054248	A549	lung:	n/a	chr5:178054145-178054154 chr5:178054143-178054155 chr5:178054218-178054227 chr5:178054226-178054238 chr5:178053444-178053458 chr5:178054228-178054237 chr5:178054226-178054238 chr5:178054227-178054237 chr5:178054143-178054155 chr5:178054227-178054236

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:178054039-178054089	MCF10A-Er-Src	breast:	n/a
2	chr5:178054039-178054089	SK-N-SH_RA	brain:	n/a
3	chr5:178054039-178054089	NB4	blood:	n/a
4	chr5:178054039-178054089	SKMC	muscle:	n/a
5	chr5:178054039-178054089	BE2_C	brain:	n/a
6	chr5:178054039-178054089	HNPCEpiC	eye:	n/a
7	chr5:178054039-178054089	HIPEpiC	eye:	n/a
8	chr5:178054039-178054089	HCT-116	colon:	n/a
9	chr5:178054039-178054089	SK-N-MC	brain:	n/a
10	chr5:178054039-178054089	PANC-1	pancreas:	n/a
11	chr5:178054039-178054089	AG09319	gingival:	n/a
12	chr5:178054039-178054089	AG04450	lung:	fetal
13	chr5:178054039-178054089	HEEpiC	esophagus:	n/a
14	chr5:178054039-178054089	PFSK-1	brain:	n/a
15	chr5:178054039-178054089	NHDF-neo	bronchial:	n/a
16	chr5:178054039-178054089	ECC-1	luminal epithelium:	n/a
17	chr5:178054039-178054089	MCF-7	breast:	n/a
18	chr5:178054039-178054089	AoSMC	blood vessel:	n/a
19	chr5:178054039-178054089	GM12878	blood:	n/a
20	chr5:178054039-178054089	AG04449	skin:	fetal
21	chr5:178054039-178054089	Hepatocyte	liver:	n/a
22	chr5:178054039-178054089	HUVEC	blood vessel:	n/a
23	chr5:178054039-178054089	HRE	kidney:	n/a
24	chr5:178054039-178054089	HAEpiC	amniotic membrane:	n/a
25	chr5:178054039-178054089	K562	blood:	n/a
26	chr5:178054039-178054089	A549	lung:	n/a
27	chr5:178054039-178054089	BJ	skin:	n/a
28	chr5:178054039-178054089	AG10803	skin:	n/a
29	chr5:178054039-178054089	HPAEpiC	pulmonary alveolar:	n/a
30	chr5:178054039-178054089	SAEC	small airway:	n/a
31	chr5:178054039-178054089	NH-A	brain:	n/a
32	chr5:178054039-178054089	IMR90	lung:	fetal
33	chr5:178054039-178054089	ProgFib	skin:	n/a
34	chr5:178054039-178054089	GM12892	blood:	n/a
35	chr5:178054039-178054089	HMEC	breast:	n/a
36	chr5:178054039-178054089	HCPEpiC	choroid plexus:	n/a
37	chr5:178054039-178054089	GM06990	blood:	n/a
38	chr5:178054039-178054089	Hela-S3	cervix:	n/a
39	chr5:178054039-178054089	HCM	heart:	n/a
40	chr5:178054039-178054089	ovcar-3	ovarian:	n/a
41	chr5:178054039-178054089	U87	brain:	n/a
42	chr5:178054039-178054089	NT2-D1	testis:	n/a
43	chr5:178054039-178054089	GM19239	blood:	n/a
44	chr5:178054039-178054089	H1-hESC	embryonic stem cell:	embryo
45	chr5:178054039-178054089	RPTEC	kidney:	n/a
46	chr5:178054039-178054089	HRCEpiC	kidney:	n/a
47	chr5:178054039-178054089	HCF	heart:	n/a
48	chr5:178054039-178054089	HepG2	liver:	n/a
49	chr5:178054039-178054089	LNCaP	prostate:	n/a
50	chr5:178054039-178054089	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178052822..178055819-chr5:178156143..178158096,2	MCF-7	breast:
2	chr5:178052987..178056050-chr5:178056072..178058258,3	MCF-7	breast:
3	chr5:177631376..177633067-chr5:178051942..178054079,2	K562	blood:
4	chr12:7052986..7053545-chr5:178053747..178054708,2	Hela-S3	cervix:
5	chr20:61568975..61569508-chr5:178053895..178054637,2	Hela-S3	cervix:
6	chr5:178053026..178055082-chr6:26156240..26159025,2	MCF-7	breast:
7	chr5:178051446..178054153-chr5:178157357..178158910,2	MCF-7	breast:
8	chr19:16770750..16771264-chr5:178053613..178054437,2	HCT-116	colon:
9	chr5:177659087..177660769-chr5:178052015..178054177,2	K562	blood:
10	chr5:177631162..177632942-chr5:178051796..178054079,4	K562	blood:
11	chr5:178053391..178055177-chr5:178285758..178288394,2	MCF-7	breast:

Variant related genes	Relation type
CLK4	TF binding region
CLK4	CpG island
ENSG00000214046	Chromatin interaction
ENSG00000113240	Chromatin interaction
ENSG00000175309	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000268790	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000101193	Chromatin interaction
ENSG00000101191	Chromatin interaction
ENSG00000178338	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3342261	chr5:178053396-178055344	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178051000-178054400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:178051000-178054600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr5:178051200-178054600	Active TSS	Aorta	Aorta
4	chr5:178051400-178054400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:178051600-178054400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:178051600-178054600	Active TSS	NHDF-Ad	bronchial
7	chr5:178051600-178054600	Active TSS	NHLF	lung
8	chr5:178051800-178054600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:178051800-178054600	Active TSS	HSMM	muscle
10	chr5:178051800-178054800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:178052000-178054200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:178052000-178054200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:178052000-178054400	Active TSS	Fetal Intestine Large	intestine
14	chr5:178052000-178054400	Active TSS	Lung	lung
15	chr5:178052000-178054600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:178052000-178054600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:178052000-178054600	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr5:178052000-178054800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:178052000-178054800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:178052000-178054800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:178052200-178054400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:178052200-178054400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:178052200-178054400	Active TSS	HMEC	breast
26	chr5:178052200-178054600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:178052200-178054600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:178052200-178054600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:178052200-178054600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:178052200-178054600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:178052200-178054600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:178052200-178054600	Active TSS	Esophagus	oesophagus
33	chr5:178052200-178054600	Active TSS	Fetal Heart	heart
34	chr5:178052200-178054600	Active TSS	Fetal Intestine Small	intestine
35	chr5:178052200-178054600	Active TSS	Fetal Kidney	kidney
36	chr5:178052200-178054800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr5:178052200-178054800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr5:178052200-178054800	Active TSS	Brain Anterior Caudate	brain
39	chr5:178052200-178054800	Active TSS	Colonic Mucosa	Colon
40	chr5:178052200-178054800	Active TSS	Colon Smooth Muscle	Colon
41	chr5:178052200-178054800	Active TSS	Fetal Brain Female	brain
42	chr5:178052200-178054800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr5:178052200-178054800	Active TSS	NH-A	brain
44	chr5:178052200-178054800	Active TSS	NHEK	skin
45	chr5:178052200-178054800	Active TSS	Osteobl	bone
46	chr5:178052400-178054200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:178052400-178054400	Active TSS	Primary T cells fromperipheralblood	blood
48	chr5:178052400-178054400	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr5:178052400-178054400	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr5:178052400-178054400	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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