Variant report

Variant	rs493894
Chromosome Location	chr1:212734994-212734995
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	SMARCC1	chr1:212734593-212735201	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:212734972-212735109	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr1:212734822-212735253	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr1:212734976-212735383	Hela-S3	cervix:	n/a	n/a
5	SP1	chr1:212734245-212735489	HCT-116	colon:	n/a	n/a
6	POLR2A	chr1:212734692-212735299	HCT-116	colon:	n/a	n/a
7	GATA3	chr1:212734616-212735213	T-47D	breast:	n/a	n/a
8	MAFK	chr1:212734773-212735055	IMR90	lung:	n/a	n/a
9	POLR2A	chr1:212734835-212735095	Hela-S3	cervix:	n/a	n/a
10	JUND	chr1:212734696-212735334	Hela-S3	cervix:	n/a	chr1:212734742-212734754
11	CEBPB	chr1:212734837-212735332	Hela-S3	cervix:	n/a	n/a
12	FOS	chr1:212734793-212735080	MCF10A-Er-Src	breast:	n/a	n/a
13	RFX5	chr1:212734753-212735357	Hela-S3	cervix:	n/a	chr1:212735071-212735086 chr1:212735071-212735084
14	CBX3	chr1:212734177-212735460	HCT-116	colon:	n/a	n/a
15	FOSL2	chr1:212734601-212735381	SK-N-SH	brain:	n/a	chr1:212734742-212734754
16	FOS	chr1:212734815-212735332	Hela-S3	cervix:	n/a	n/a
17	EP300	chr1:212734631-212735384	ECC-1	luminal epithelium:	n/a	chr1:212734735-212734742
18	SMC3	chr1:212734799-212735262	Hela-S3	cervix:	n/a	n/a
19	FOS	chr1:212734871-212735199	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr1:212734811-212735261	Hela-S3	cervix:	n/a	n/a
21	YY1	chr1:212734769-212735027	HCT-116	colon:	n/a	n/a
22	TCF12	chr1:212734659-212735408	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr1:212734860-212735010	HCPEpiC	choroid plexus:	n/a	n/a
24	POLR2A	chr1:212734794-212735152	Hela-S3	cervix:	n/a	n/a
25	FOS	chr1:212734763-212735215	MCF10A-Er-Src	breast:	n/a	n/a
26	GTF2F1	chr1:212734650-212735216	Hela-S3	cervix:	n/a	n/a
27	FOSL1	chr1:212734611-212735454	HCT-116	colon:	n/a	chr1:212734742-212734754
28	FOSL1	chr1:212734484-212735554	HCT-116	colon:	n/a	chr1:212734742-212734754
29	EP300	chr1:212734811-212735348	Hela-S3	cervix:	n/a	n/a
30	FOS	chr1:212734761-212735314	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr1:212734595-212735499	HCT-116	colon:	n/a	chr1:212734742-212734754
32	MAFK	chr1:212734801-212735374	Hela-S3	cervix:	n/a	n/a
33	MAX	chr1:212734817-212735285	Hela-S3	cervix:	n/a	n/a
34	TEAD4	chr1:212734674-212735426	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr1:212734791-212735111	HCT-116	colon:	n/a	n/a
36	JUND	chr1:212734653-212735384	SK-N-SH	brain:	n/a	chr1:212734742-212734754
37	JUND	chr1:212734523-212735478	HCT-116	colon:	n/a	chr1:212734742-212734754

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
3	chr1:212734422..212735324-chr2:162954257..162954966,2	HCT-116	colon:

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1195473	1.00[YRI][hapmap]
rs1195474	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1617473	0.86[ASN][1000 genomes]
rs2137424	0.85[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3106401	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3125291	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs484529	0.83[ASN][1000 genomes]
rs516748	0.88[ASN][1000 genomes]
rs556847	0.92[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs585428	0.83[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs599028	0.83[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs631569	0.83[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs635822	0.83[ASN][1000 genomes]
rs6702959	0.80[ASN][1000 genomes]
rs685330	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs493894	CENPF	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212732400-212736000	Enhancers	Placenta	Placenta
2	chr1:212732800-212735000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:212732800-212735000	Weak transcription	HMEC	breast
4	chr1:212732800-212738000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:212732800-212739600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:212732800-212739600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:212732800-212739800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:212732800-212739800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:212732800-212739800	Weak transcription	Stomach Mucosa	stomach
10	chr1:212732800-212740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:212733000-212735000	Weak transcription	NHEK	skin
12	chr1:212733000-212739600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:212733000-212739600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:212733000-212739800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:212733000-212739800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:212733000-212740600	Weak transcription	Fetal Heart	heart
17	chr1:212733200-212739600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:212733400-212735000	Weak transcription	K562	blood
19	chr1:212733800-212735200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:212734000-212735000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:212734200-212735000	Enhancers	NHDF-Ad	bronchial
22	chr1:212734200-212735400	Enhancers	HSMMtube	muscle
23	chr1:212734200-212735600	Enhancers	NH-A	brain
24	chr1:212734200-212736200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:212734400-212735200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:212734400-212735200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:212734400-212735200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:212734400-212735600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:212734400-212735600	Enhancers	HUVEC	blood vessel
30	chr1:212734400-212740000	Weak transcription	Aorta	Aorta
31	chr1:212734600-212735200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:212734600-212735200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:212734600-212735200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:212734600-212735200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:212734600-212735200	Flanking Active TSS	A549	lung
36	chr1:212734600-212735200	Flanking Active TSS	Hela-S3	cervix
37	chr1:212734600-212735400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:212734600-212735800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:212734800-212735000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:212734800-212735000	Enhancers	Fetal Muscle Leg	muscle
41	chr1:212734800-212735000	Enhancers	Stomach Smooth Muscle	stomach
42	chr1:212734800-212735200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr1:212734800-212735200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:212734800-212735200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:212734800-212735200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:212734800-212735200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:212734800-212735200	Enhancers	Left Ventricle	heart
48	chr1:212734800-212735200	Enhancers	Right Atrium	heart
49	chr1:212734800-212735200	Flanking Active TSS	HSMM	muscle
50	chr1:212734800-212735200	Flanking Active TSS	NHLF	lung

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