Variant report

Variant	rs13447454
Chromosome Location	chr1:91966406-91966407
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	POLR2A	chr1:91965297-91967439	SK-N-MC	brain:	n/a	n/a
2	GTF2B	chr1:91966153-91966909	K562	blood:	n/a	n/a
3	HA-E2F1	chr1:91965956-91967314	MCF-7	breast:	n/a	chr1:91966631-91966643 chr1:91966600-91966609 chr1:91966302-91966314 chr1:91966648-91966657 chr1:91966393-91966403 chr1:91966635-91966642 chr1:91966601-91966608 chr1:91966601-91966608 chr1:91966596-91966611 chr1:91966635-91966642 chr1:91966376-91966385 chr1:91966395-91966407 chr1:91966600-91966612 chr1:91966635-91966642 chr1:91966411-91966420 chr1:91966601-91966608
4	CEBPB	chr1:91966105-91966500	K562	blood:	n/a	n/a
5	HEY1	chr1:91966158-91966927	HepG2	liver:	n/a	n/a
6	TEAD4	chr1:91966057-91967444	K562	blood:	n/a	n/a
7	MAX	chr1:91966016-91967318	SK-N-SH	brain:	n/a	chr1:91967048-91967058
8	TRIM28	chr1:91966142-91967315	K562	blood:	n/a	n/a
9	MAX	chr1:91965938-91967469	A549	lung:	n/a	chr1:91967048-91967058
10	REST	chr1:91966097-91967131	PFSK-1	brain:	n/a	n/a
11	MXI1	chr1:91966404-91967198	K562	blood:	n/a	n/a
12	POLR2A	chr1:91966094-91967254	HCT-116	colon:	n/a	n/a
13	MAX	chr1:91966204-91967278	K562	blood:	n/a	chr1:91967048-91967058
14	TAF1	chr1:91966107-91967079	K562	blood:	n/a	n/a
15	TBP	chr1:91966155-91966759	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr1:91966140-91967271	PANC-1	pancreas:	n/a	n/a
17	E2F4	chr1:91966104-91967120	K562	blood:	n/a	chr1:91966579-91966590 chr1:91966631-91966643 chr1:91966600-91966609 chr1:91966302-91966314 chr1:91966648-91966657 chr1:91966393-91966403 chr1:91966635-91966642 chr1:91966601-91966608 chr1:91966601-91966608 chr1:91966596-91966611 chr1:91966632-91966643 chr1:91966635-91966642 chr1:91966376-91966385 chr1:91966395-91966407 chr1:91966600-91966612 chr1:91966635-91966642 chr1:91966599-91966610 chr1:91966411-91966420 chr1:91966601-91966608
18	NFATC1	chr1:91966370-91967015	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:91965502-91967438	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr1:91966311-91966608	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:91965298-91968039	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:91966400-91966550	HPAF	blood vessel:	n/a	n/a
23	ZNF384	chr1:91966390-91967961	K562	blood:	n/a	n/a
24	STAT3	chr1:91965949-91967091	MCF10A-Er-Src	breast:	n/a	chr1:91966200-91966214 chr1:91966273-91966281 chr1:91966197-91966217 chr1:91966201-91966212 chr1:91966203-91966212 chr1:91966202-91966211
25	ELF1	chr1:91966115-91967077	K562	blood:	n/a	n/a
26	MXI1	chr1:91966192-91967162	HepG2	liver:	n/a	n/a
27	CEBPB	chr1:91965911-91966739	K562	blood:	n/a	n/a
28	CEBPD	chr1:91966064-91966800	K562	blood:	n/a	n/a
29	GABPA	chr1:91966227-91967100	K562	blood:	n/a	chr1:91966410-91966424 chr1:91966649-91966658 chr1:91966647-91966658 chr1:91966372-91966386 chr1:91966407-91966421 chr1:91966410-91966421 chr1:91966644-91966658 chr1:91966410-91966419 chr1:91966375-91966386 chr1:91966375-91966384 chr1:91966647-91966661
30	KAP1	chr1:91965606-91967313	U2OS	brain:	n/a	n/a
31	POLR2A	chr1:91965700-91967369	GM18526	blood:	n/a	n/a
32	CEBPD	chr1:91966139-91966476	HepG2	liver:	n/a	n/a
33	SP4	chr1:91966192-91967109	H1-hESC	embryonic stem cell:	n/a	chr1:91966601-91966617
34	SP1	chr1:91966321-91967459	H1-hESC	embryonic stem cell:	n/a	chr1:91967129-91967136 chr1:91966603-91966612
35	EP300	chr1:91966213-91966925	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:91966188-91967140	A549	lung:	n/a	n/a
37	MAX	chr1:91966155-91967298	MCF-7	breast:	n/a	chr1:91967048-91967058
38	TAF1	chr1:91966114-91967287	GM12878	blood:	n/a	n/a
39	ATF3	chr1:91966112-91966580	A549	lung:	n/a	n/a
40	ZMIZ1	chr1:91966043-91967171	K562	blood:	n/a	n/a
41	POLR2A	chr1:91966255-91966517	HepG2	liver:	n/a	n/a
42	NFIC	chr1:91966229-91967321	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr1:91966131-91967314	GM12891	blood:	n/a	n/a
44	POLR2A	chr1:91966136-91967204	A549	lung:	n/a	n/a
45	POLR2A	chr1:91965536-91967735	K562	blood:	n/a	n/a
46	POLR2A	chr1:91965922-91967411	GM12892	blood:	n/a	n/a
47	TCF7L2	chr1:91966218-91967175	HCT-116	colon:	n/a	n/a
48	SP1	chr1:91966372-91967360	H1-hESC	embryonic stem cell:	n/a	chr1:91967129-91967136 chr1:91966603-91966612
49	EP300	chr1:91965988-91967200	GM12878	blood:	n/a	chr1:91966076-91966085 chr1:91966075-91966089
50	CEBPB	chr1:91965982-91967101	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:91966377-91966427	A549	lung:	n/a
2	chr1:91966400-91966450	HIPEpiC	eye:	n/a
3	chr1:91966361-91966411	NHBE	bronchial:	n/a
4	chr1:91966400-91966450	GM12891	blood:	n/a
5	chr1:91966361-91966411	HMEC	breast:	n/a
6	chr1:91966377-91966427	HEEpiC	esophagus:	n/a
7	chr1:91966377-91966427	PFSK-1	brain:	n/a
8	chr1:91966361-91966411	HCF	heart:	n/a
9	chr1:91966361-91966411	SK-N-SH_RA	brain:	n/a
10	chr1:91966400-91966450	AG10803	skin:	n/a
11	chr1:91966361-91966411	HCT-116	colon:	n/a
12	chr1:91966361-91966411	SAEC	small airway:	n/a
13	chr1:91966361-91966411	CMK	blood:	n/a
14	chr1:91966400-91966450	HL-60	blood:	n/a
15	chr1:91966377-91966427	AoSMC	blood vessel:	n/a
16	chr1:91966377-91966427	AG10803	skin:	n/a
17	chr1:91966377-91966427	SK-N-MC	brain:	n/a
18	chr1:91966377-91966427	AG04449	skin:	fetal
19	chr1:91966400-91966450	Hepatocyte	liver:	n/a
20	chr1:91966361-91966411	LNCaP	prostate:	n/a
21	chr1:91966361-91966411	NB4	blood:	n/a
22	chr1:91966377-91966427	NHDF-neo	bronchial:	n/a
23	chr1:91966361-91966411	A549	lung:	n/a
24	chr1:91966377-91966427	Caco-2	colon:	n/a
25	chr1:91966361-91966411	AG04450	lung:	fetal
26	chr1:91966377-91966427	AG09309	skin:	n/a
27	chr1:91966361-91966411	HUVEC	blood vessel:	n/a
28	chr1:91966400-91966450	HUVEC	blood vessel:	n/a
29	chr1:91966400-91966450	SK-N-SH	brain:	n/a
30	chr1:91966400-91966450	K562	blood:	n/a
31	chr1:91966377-91966427	HRCEpiC	kidney:	n/a
32	chr1:91966400-91966450	HRE	kidney:	n/a
33	chr1:91966361-91966411	SK-N-MC	brain:	n/a
34	chr1:91966400-91966450	AoSMC	blood vessel:	n/a
35	chr1:91966377-91966427	GM12892	blood:	n/a
36	chr1:91966400-91966450	SAEC	small airway:	n/a
37	chr1:91966377-91966427	ECC-1	luminal epithelium:	n/a
38	chr1:91966361-91966411	HRCEpiC	kidney:	n/a
39	chr1:91966400-91966450	HepG2	liver:	n/a
40	chr1:91966400-91966450	HCM	heart:	n/a
41	chr1:91966361-91966411	AoSMC	blood vessel:	n/a
42	chr1:91966377-91966427	NHBE	bronchial:	n/a
43	chr1:91966361-91966411	BE2_C	brain:	n/a
44	chr1:91966361-91966411	NT2-D1	testis:	n/a
45	chr1:91966400-91966450	HRPEpiC	eye:	n/a
46	chr1:91966361-91966411	NH-A	brain:	n/a
47	chr1:91966361-91966411	Hela-S3	cervix:	n/a
48	chr1:91966377-91966427	NB4	blood:	n/a
49	chr1:91966400-91966450	U87	brain:	n/a
50	chr1:91966361-91966411	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:91869685..91873685-chr1:91965673..91969192,5	K562	blood:
2	chr1:91966232..91966769-chr14:23475694..23476368,2	Hela-S3	cervix:
3	chr1:91867702..91872217-chr1:91965179..91968319,5	K562	blood:
4	chr1:91870066..91871690-chr1:91965545..91967764,2	MCF-7	breast:
5	chr1:91966057..91966769-chr10:1094298..1095218,2	Hela-S3	cervix:
6	chr1:91966304..91966898-chr16:30406443..30407227,2	Hela-S3	cervix:

Variant related genes	Relation type
CDC7	TF binding region
CDC7	CpG island
ENSG00000067064	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000162669	Chromatin interaction
ENSG00000100802	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11164839	0.81[GIH][hapmap];0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs11584206	1.00[ASN][1000 genomes]
rs11585309	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085185	1.00[ASN][1000 genomes]
rs2893171	1.00[ASN][1000 genomes]
rs61798798	1.00[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13447454	CDC7	cis	multi-tissue	Pritchard
rs13447454	CDC7	cis	Thyroid	GTEx
rs13447454	CDC7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91965200-91966600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:91965600-91966600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:91965600-91967600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:91965600-91967600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:91965600-91968000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:91965800-91966600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:91965800-91967000	Active TSS	Brain Hippocampus Middle	brain
8	chr1:91965800-91967200	Active TSS	Colonic Mucosa	Colon
9	chr1:91965800-91967200	Active TSS	Fetal Lung	lung
10	chr1:91965800-91967200	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:91965800-91967200	Active TSS	Right Ventricle	heart
12	chr1:91965800-91967400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:91965800-91967400	Active TSS	Right Atrium	heart
14	chr1:91965800-91967600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:91965800-91967600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:91965800-91967600	Active TSS	Fetal Brain Male	brain
17	chr1:91965800-91967600	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:91965800-91967800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr1:91965800-91967800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:91965800-91967800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:91965800-91967800	Active TSS	HSMM	muscle
22	chr1:91965800-91968200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:91965800-91968400	Active TSS	Fetal Brain Female	brain
24	chr1:91966000-91966600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr1:91966000-91967000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:91966000-91967000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:91966000-91967000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:91966000-91967000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr1:91966000-91967000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr1:91966000-91967000	Active TSS	Adipose Nuclei	Adipose
31	chr1:91966000-91967200	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr1:91966000-91967200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:91966000-91967200	Active TSS	Esophagus	oesophagus
34	chr1:91966000-91967200	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr1:91966000-91967200	Active TSS	Small Intestine	intestine
36	chr1:91966000-91967400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:91966000-91967400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:91966000-91967400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:91966000-91967400	Active TSS	Fetal Stomach	stomach
40	chr1:91966000-91967400	Active TSS	Left Ventricle	heart
41	chr1:91966000-91967400	Active TSS	Lung	lung
42	chr1:91966000-91967400	Active TSS	Ovary	ovary
43	chr1:91966000-91967400	Active TSS	Pancreas	Pancrea
44	chr1:91966000-91967400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:91966000-91967400	Active TSS	Psoas Muscle	Psoas
46	chr1:91966000-91967600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:91966000-91967600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr1:91966000-91967600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:91966000-91967600	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:91966000-91967600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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