Variant report

Variant	rs73351824
Chromosome Location	chr5:178054459-178054460
allele	C/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	ZNF384	chr5:178052770-178054463	K562	blood:	n/a	n/a
2	POLR2A	chr5:178053049-178054494	GM19099	blood:	n/a	n/a
3	POLR2A	chr5:178053171-178054584	Hela-S3	cervix:	n/a	n/a
4	BHLHE40	chr5:178052939-178054553	GM12878	blood:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054544-178054553
5	MYC	chr5:178052572-178054553	K562	blood:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054544-178054553 chr5:178054333-178054340
6	TBL1XR1	chr5:178053274-178054539	GM12878	blood:	n/a	n/a
7	USF1	chr5:178053861-178054695	ECC-1	luminal epithelium:	n/a	chr5:178054543-178054552 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
8	POLR2A	chr5:178052968-178054585	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr5:178053265-178054482	ECC-1	luminal epithelium:	n/a	n/a
10	NRF1	chr5:178053954-178054662	H1-hESC	embryonic stem cell:	n/a	chr5:178054189-178054203 chr5:178054228-178054237 chr5:178054099-178054110
11	POLR2A	chr5:178052757-178054569	GM12878	blood:	n/a	n/a
12	HCFC1	chr5:178053469-178054626	K562	blood:	n/a	n/a
13	USF2	chr5:178053918-178054677	Hela-S3	cervix:	n/a	chr5:178054543-178054552 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
14	STAT3	chr5:178053277-178054480	MCF10A-Er-Src	breast:	n/a	chr5:178054223-178054235 chr5:178054217-178054229 chr5:178054219-178054231
15	POLR2A	chr5:178053501-178054527	HCT-116	colon:	n/a	n/a
16	UBTF	chr5:178053059-178054461	K562	blood:	n/a	n/a
17	ZNF143	chr5:178053433-178054706	K562	blood:	n/a	n/a
18	MYC	chr5:178053969-178054687	H1-hESC	embryonic stem cell:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054543-178054554 chr5:178054544-178054553 chr5:178054543-178054554 chr5:178054333-178054340
19	MAX	chr5:178053432-178054657	HUVEC	blood vessel:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054543-178054554 chr5:178054544-178054553 chr5:178054543-178054554 chr5:178054333-178054340
20	BHLHE40	chr5:178052960-178054712	K562	blood:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
21	POLR2A	chr5:178053044-178054582	Raji	blood:	n/a	n/a
22	FOS	chr5:178054455-178054464	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr5:178053108-178054471	HEK293	kidney:	n/a	n/a
24	USF1	chr5:178053380-178054707	HCT-116	colon:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
25	POLR2A	chr5:178052458-178054533	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:178052944-178054494	K562	blood:	n/a	n/a
27	MYC	chr5:178052573-178054577	MCF10A-Er-Src	breast:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054543-178054554 chr5:178054544-178054553 chr5:178054543-178054554 chr5:178054333-178054340
28	KAP1	chr5:178054273-178054827	HEK293	kidney:	n/a	n/a
29	USF2	chr5:178053453-178054623	GM12878	blood:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
30	WRNIP1	chr5:178054421-178054951	GM12878	blood:	n/a	n/a
31	MXI1	chr5:178052778-178054504	Hela-S3	cervix:	n/a	chr5:178054156-178054165
32	POLR2A	chr5:178052335-178054585	GM18505	blood:	n/a	n/a
33	POLR2A	chr5:178051355-178054657	HepG2	liver:	n/a	n/a
34	USF1	chr5:178054274-178054749	H1-hESC	embryonic stem cell:	n/a	chr5:178054543-178054552 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
35	POLR2A	chr5:178053110-178054496	GM15510	blood:	n/a	n/a
36	MAZ	chr5:178051632-178054946	IMR90	lung:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054543-178054554 chr5:178054544-178054553 chr5:178054543-178054554 chr5:178054333-178054340
37	MAX	chr5:178053922-178054520	A549	lung:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054333-178054340
38	CBX3	chr5:178054231-178054818	K562	blood:	n/a	n/a
39	MXI1	chr5:178053175-178054466	HepG2	liver:	n/a	chr5:178054156-178054165
40	SETDB1	chr5:178054331-178054677	U2OS	brain:	n/a	n/a
41	POLR2A	chr5:178052999-178054519	H1-neurons	neurons:	n/a	n/a
42	MAX	chr5:178053482-178054485	HepG2	liver:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054333-178054340
43	POLR2A	chr5:178053249-178054510	GM18526	blood:	n/a	n/a
44	USF1	chr5:178053750-178054700	HCT-116	colon:	n/a	chr5:178054543-178054552 chr5:178054544-178054553 chr5:178054538-178054559 chr5:178054544-178054553
45	ZNF143	chr5:178053307-178054592	GM12878	blood:	n/a	n/a
46	YY1	chr5:178053297-178054523	HepG2	liver:	n/a	chr5:178054040-178054054 chr5:178054193-178054204 chr5:178054038-178054049 chr5:178054020-178054042 chr5:178054032-178054042 chr5:178054225-178054234 chr5:178054032-178054042 chr5:178054031-178054039
47	TAF1	chr5:178053202-178054563	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3A	chr5:178052606-178054564	H1-hESC	embryonic stem cell:	n/a	chr5:178054193-178054204
49	CTCF	chr5:178054408-178054495	K562	blood:	n/a	n/a
50	CREB1	chr5:178053801-178054519	A549	lung:	n/a	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	chr12:7052986..7053545-chr5:178053747..178054708,2	Hela-S3	cervix:
4	chr5:178054261..178056030-chr5:178057503..178059124,2	MCF-7	breast:
5	chr20:61568975..61569508-chr5:178053895..178054637,2	Hela-S3	cervix:
6	chr5:178053026..178055082-chr6:26156240..26159025,2	MCF-7	breast:
7	chr5:178054153..178056905-chr5:178057584..178060537,3	K562	blood:
8	chr5:178053391..178055177-chr5:178285758..178288394,2	MCF-7	breast:

Variant related genes	Relation type
CLK4	TF binding region
ENSG00000101193	Chromatin interaction
ENSG00000178338	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000169131	Chromatin interaction
ENSG00000113240	Chromatin interaction
ENSG00000101191	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs58683268	0.83[AFR][1000 genomes]
rs60822440	1.00[AFR][1000 genomes]
rs73348406	1.00[AFR][1000 genomes]
rs73350301	1.00[AFR][1000 genomes]
rs73351821	0.83[AFR][1000 genomes]
rs73351831	0.88[AFR][1000 genomes]
rs73353820	0.83[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	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	chr5:178051000-178054600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:178051200-178054600	Active TSS	Aorta	Aorta
3	chr5:178051600-178054600	Active TSS	NHDF-Ad	bronchial
4	chr5:178051600-178054600	Active TSS	NHLF	lung
5	chr5:178051800-178054600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:178051800-178054600	Active TSS	HSMM	muscle
7	chr5:178051800-178054800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:178052000-178054600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:178052000-178054600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:178052000-178054600	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr5:178052000-178054800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:178052000-178054800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:178052000-178054800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:178052200-178054600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:178052200-178054600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:178052200-178054600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:178052200-178054600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:178052200-178054600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:178052200-178054600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:178052200-178054600	Active TSS	Esophagus	oesophagus
23	chr5:178052200-178054600	Active TSS	Fetal Heart	heart
24	chr5:178052200-178054600	Active TSS	Fetal Intestine Small	intestine
25	chr5:178052200-178054600	Active TSS	Fetal Kidney	kidney
26	chr5:178052200-178054800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr5:178052200-178054800	Active TSS	Muscle Satellite Cultured Cells	--
28	chr5:178052200-178054800	Active TSS	Brain Anterior Caudate	brain
29	chr5:178052200-178054800	Active TSS	Colonic Mucosa	Colon
30	chr5:178052200-178054800	Active TSS	Colon Smooth Muscle	Colon
31	chr5:178052200-178054800	Active TSS	Fetal Brain Female	brain
32	chr5:178052200-178054800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:178052200-178054800	Active TSS	NH-A	brain
34	chr5:178052200-178054800	Active TSS	NHEK	skin
35	chr5:178052200-178054800	Active TSS	Osteobl	bone
36	chr5:178052400-178054600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr5:178052400-178054600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:178052400-178054600	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr5:178052400-178054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:178052400-178054600	Active TSS	Fetal Brain Male	brain
41	chr5:178052400-178054600	Active TSS	Fetal Stomach	stomach
42	chr5:178052400-178054600	Active TSS	Gastric	stomach
43	chr5:178052400-178054600	Active TSS	Left Ventricle	heart
44	chr5:178052400-178054600	Active TSS	Ovary	ovary
45	chr5:178052400-178054600	Active TSS	Pancreas	Pancrea
46	chr5:178052400-178054600	Active TSS	Psoas Muscle	Psoas
47	chr5:178052400-178054600	Active TSS	Right Atrium	heart
48	chr5:178052400-178054600	Active TSS	HSMMtube	muscle
49	chr5:178052400-178054800	Active TSS	Brain Angular Gyrus	brain
50	chr5:178052400-178054800	Active TSS	Duodenum Mucosa	Duodenum

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