Variant report

Variant	rs16853551
Chromosome Location	chr1:178994534-178994535
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	EGR1	chr1:178994406-178996036	HCT-116	colon:	n/a	chr1:178995078-178995091 chr1:178995015-178995025 chr1:178995104-178995118 chr1:178994836-178994845 chr1:178995018-178995031
2	POLR2A	chr1:178994316-178996287	K562	blood:	n/a	n/a
3	YY1	chr1:178994380-178995080	H1-hESC	embryonic stem cell:	n/a	chr1:178994812-178994826 chr1:178995018-178995027 chr1:178994908-178994922 chr1:178994812-178994821
4	TAF7	chr1:178994471-178995023	H1-hESC	embryonic stem cell:	n/a	n/a
5	SMARCB1	chr1:178994232-178995968	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr1:178994405-178996650	IMR90	lung:	n/a	chr1:178995016-178995026
7	MAX	chr1:178994467-178996244	A549	lung:	n/a	chr1:178995016-178995026
8	ETS1	chr1:178994519-178995914	K562	blood:	n/a	chr1:178995016-178995027 chr1:178995720-178995731
9	TEAD4	chr1:178994358-178996645	K562	blood:	n/a	chr1:178996267-178996276
10	POLR2A	chr1:178994470-178995115	SK-N-MC	brain:	n/a	n/a
11	CTCF	chr1:178994407-178994989	K562	blood:	n/a	chr1:178994908-178994921
12	POLR2A	chr1:178994029-178996204	K562	blood:	n/a	n/a
13	POLR2A	chr1:178994327-178996348	Hela-S3	cervix:	n/a	n/a
14	USF2	chr1:178994234-178994613	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF12	chr1:178994213-178995132	A549	lung:	n/a	n/a
16	SP1	chr1:178994448-178995613	A549	lung:	n/a	chr1:178995014-178995026 chr1:178995311-178995320 chr1:178995082-178995093 chr1:178995015-178995024 chr1:178995027-178995037 chr1:178994727-178994741
17	ZNF143	chr1:178994183-178995707	H1-hESC	embryonic stem cell:	n/a	chr1:178994833-178994843
18	CBX3	chr1:178993860-178995888	K562	blood:	n/a	n/a
19	JUN	chr1:178994384-178995458	K562	blood:	n/a	chr1:178995018-178995027 chr1:178994770-178994779
20	MYC	chr1:178994158-178996280	A549	lung:	n/a	chr1:178995016-178995026
21	IRF1	chr1:178994093-178997271	K562	blood:	n/a	chr1:178997164-178997181 chr1:178994771-178994780 chr1:178997184-178997191 chr1:178996939-178996952 chr1:178996142-178996156
22	EGR1	chr1:178994513-178996074	HCT-116	colon:	n/a	chr1:178995078-178995091 chr1:178995015-178995025 chr1:178995104-178995118 chr1:178994836-178994845 chr1:178995018-178995031
23	CHD2	chr1:178994420-178995923	K562	blood:	n/a	n/a
24	MYC	chr1:178994488-178996305	K562	blood:	n/a	chr1:178995016-178995026
25	SP1	chr1:178994468-178995988	HCT-116	colon:	n/a	chr1:178995014-178995026 chr1:178995311-178995320 chr1:178995082-178995093 chr1:178995750-178995764 chr1:178995015-178995024 chr1:178995027-178995037 chr1:178994727-178994741
26	TCF7L2	chr1:178994438-178996031	Hela-S3	cervix:	n/a	n/a
27	JUND	chr1:178994251-178996392	SK-N-SH	brain:	n/a	chr1:178995018-178995027 chr1:178994770-178994779
28	MTA3	chr1:178994487-178995053	GM12878	blood:	n/a	n/a
29	JUND	chr1:178994379-178996095	GM12878	blood:	n/a	chr1:178995018-178995027 chr1:178994770-178994779
30	HCFC1	chr1:178994281-178996202	K562	blood:	n/a	n/a
31	TAF1	chr1:178994465-178995121	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:178994141-178996923	Raji	blood:	n/a	n/a
33	GATA1	chr1:178994262-178994996	PBDE	blood:	n/a	chr1:178994769-178994779 chr1:178994704-178994714
34	ZNF143	chr1:178994262-178995119	Hela-S3	cervix:	n/a	chr1:178994833-178994843
35	USF2	chr1:178994232-178994665	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:178993511-178997453	K562	blood:	n/a	n/a
37	RCOR1	chr1:178994127-178996805	K562	blood:	n/a	n/a
38	CBX3	chr1:178994049-178994888	K562	blood:	n/a	n/a
39	CREB1	chr1:178994522-178996430	K562	blood:	n/a	n/a
40	TRIM28	chr1:178994043-178995189	K562	blood:	n/a	n/a
41	POLR2A	chr1:178992621-178996965	PBDE	blood:	n/a	n/a
42	CHD1	chr1:178994317-178996876	IMR90	lung:	n/a	n/a
43	UBTF	chr1:178994346-178996250	K562	blood:	n/a	n/a
44	POLR2A	chr1:178994518-178996644	HepG2	liver:	n/a	n/a
45	HA-E2F1	chr1:178994337-178996202	MCF-7	breast:	n/a	chr1:178995015-178995024 chr1:178995678-178995692 chr1:178995310-178995319 chr1:178995284-178995295 chr1:178994833-178994843 chr1:178994836-178994845 chr1:178994812-178994821
46	TBP	chr1:178994515-178996391	K562	blood:	n/a	n/a
47	NFYA	chr1:178994169-178995124	K562	blood:	n/a	n/a
48	MYC	chr1:178994482-178996056	NB4	blood:	n/a	chr1:178995016-178995026
49	TBL1XR1	chr1:178994150-178995153	K562	blood:	n/a	n/a
50	E2F6	chr1:178994314-178996164	K562	blood:	n/a	chr1:178995015-178995024 chr1:178995678-178995692 chr1:178995310-178995319 chr1:178994833-178994843 chr1:178994836-178994845 chr1:178994812-178994821 chr1:178995285-178995296

No.	Distal block	Cell Line	Cell type
1	chr1:178994037..178996559-chr6:26216842..26218993,2	MCF-7	breast:
2	chr1:178510389..178513760-chr1:178993228..178995789,4	MCF-7	breast:
3	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
4	chr1:178991699..178994582-chr1:179050061..179052704,4	MCF-7	breast:
5	chr1:178693031..178696022-chr1:178993845..178996341,3	MCF-7	breast:

Variant related genes	Relation type
FAM20B	TF binding region
ENSG00000187990	Chromatin interaction
ENSG00000184909	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000213057	Chromatin interaction
ENSG00000273062	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000116191	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10157463	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158768	0.81[ASN][1000 genomes]
rs10913675	0.97[ASN][1000 genomes]
rs10913687	0.97[ASN][1000 genomes]
rs11801262	0.90[EUR][1000 genomes]
rs11802142	0.81[EUR][1000 genomes]
rs11804174	0.81[EUR][1000 genomes]
rs11808217	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064695	0.87[EUR][1000 genomes]
rs12066589	0.97[ASN][1000 genomes]
rs12067262	0.97[ASN][1000 genomes]
rs12071751	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075028	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12076957	0.97[ASN][1000 genomes]
rs12079974	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083856	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086225	0.97[ASN][1000 genomes]
rs12089188	0.97[ASN][1000 genomes]
rs12091355	0.94[ASN][1000 genomes]
rs16853619	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274228	0.83[ASN][1000 genomes]
rs3766631	0.97[ASN][1000 genomes]
rs3766633	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766634	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45499094	0.83[ASN][1000 genomes]
rs57215421	1.00[ASN][1000 genomes]
rs58726191	0.97[ASN][1000 genomes]
rs72707289	0.90[EUR][1000 genomes]
rs72707290	0.90[EUR][1000 genomes]
rs72707297	0.81[EUR][1000 genomes]
rs72709407	0.81[EUR][1000 genomes]
rs72709410	0.81[EUR][1000 genomes]
rs72709411	0.81[EUR][1000 genomes]
rs72709420	0.81[EUR][1000 genomes]
rs72709430	0.81[EUR][1000 genomes]
rs72709434	0.81[EUR][1000 genomes]
rs72709443	0.81[EUR][1000 genomes]
rs7516491	0.97[ASN][1000 genomes]
rs7519023	0.97[ASN][1000 genomes]
rs7552470	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725888	0.94[ASN][1000 genomes]
rs9726948	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9730271	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420967	chr1:178993954-178996502	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	esv3396952	chr1:178994279-178996377	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178989200-178994600	Weak transcription	Esophagus	oesophagus
2	chr1:178989600-178994600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:178991400-178994600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:178993400-178994800	Flanking Active TSS	K562	blood
5	chr1:178993600-178994800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr1:178994000-178994600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:178994000-178994600	Flanking Active TSS	Fetal Intestine Large	intestine
8	chr1:178994000-178994600	Flanking Active TSS	Fetal Intestine Small	intestine
9	chr1:178994000-178996200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:178994000-178996400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:178994200-178994600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr1:178994200-178994600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:178994200-178994600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:178994200-178994600	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr1:178994200-178994600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr1:178994200-178994600	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr1:178994200-178994600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr1:178994200-178994600	Flanking Active TSS	A549	lung
19	chr1:178994200-178994600	Flanking Active TSS	Hela-S3	cervix
20	chr1:178994200-178994600	Flanking Active TSS	HepG2	liver
21	chr1:178994200-178994600	Flanking Active TSS	NHLF	lung
22	chr1:178994200-178994600	Flanking Active TSS	Osteobl	bone
23	chr1:178994200-178994800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:178994200-178994800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr1:178994200-178994800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:178994200-178994800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:178994200-178994800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:178994200-178994800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:178994200-178994800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:178994200-178994800	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr1:178994200-178994800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:178994200-178994800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:178994200-178994800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr1:178994200-178994800	Flanking Active TSS	Dnd41	blood
37	chr1:178994200-178994800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:178994200-178995400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:178994200-178996000	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:178994200-178996000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:178994200-178996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:178994200-178996000	Active TSS	Brain Hippocampus Middle	brain
43	chr1:178994200-178996000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:178994200-178996000	Active TSS	Rectal Smooth Muscle	rectum
45	chr1:178994200-178996200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:178994200-178996200	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:178994200-178996200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:178994200-178996200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:178994200-178996200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:178994200-178996200	Active TSS	Fetal Lung	lung

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