Variant report

Variant	rs5744134
Chromosome Location	chr1:223311003-223311004
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	CEBPB	chr1:223310766-223311014	HepG2	liver:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
2	STAT3	chr1:223310779-223311103	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:223310778-223311103	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:223310596-223311257	MCF-7	breast:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
5	CEBPB	chr1:223310567-223311249	HCT-116	colon:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
6	CEBPB	chr1:223310731-223311126	IMR90	lung:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
7	STAT3	chr1:223310685-223311145	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:223310742-223311095	MCF10A-Er-Src	breast:	n/a	chr1:223310807-223310819
9	CEBPB	chr1:223310667-223311153	Hela-S3	cervix:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
10	USF2	chr1:223310845-223311125	Hela-S3	cervix:	n/a	n/a
11	FOS	chr1:223310766-223311084	MCF10A-Er-Src	breast:	n/a	chr1:223310807-223310819
12	CEBPB	chr1:223310742-223311242	A549	lung:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
13	STAT3	chr1:223310762-223311187	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:223310659-223311108	SK-N-MC	brain:	n/a	n/a
15	CEBPB	chr1:223310682-223311219	HCT-116	colon:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
16	CEBPB	chr1:223310795-223311029	HepG2	liver:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
17	E2F4	chr1:223310835-223311234	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr1:223310681-223311207	K562	blood:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
19	CEBPB	chr1:223310718-223311111	HepG2	liver:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
20	CEBPB	chr1:223310769-223311012	K562	blood:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
21	CEBPB	chr1:223310746-223311105	HepG2	liver:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
22	FOS	chr1:223310777-223311068	MCF10A-Er-Src	breast:	n/a	chr1:223310807-223310819
23	MYC	chr1:223310816-223311081	MCF10A-Er-Src	breast:	n/a	n/a
24	CEBPB	chr1:223310738-223311139	K562	blood:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
25	CEBPB	chr1:223310670-223311189	A549	lung:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
26	FOS	chr1:223310753-223311079	MCF10A-Er-Src	breast:	n/a	chr1:223310807-223310819
27	CEBPB	chr1:223310731-223311118	A549	lung:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
28	GATA3	chr1:223310889-223311075	SH-SY5Y	brain:	n/a	chr1:223310999-223311009
29	CEBPB	chr1:223310661-223311174	ECC-1	luminal epithelium:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
30	CEBPB	chr1:223310772-223311078	H1-hESC	embryonic stem cell:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
31	MYC	chr1:223310769-223311108	MCF10A-Er-Src	breast:	n/a	n/a
32	EP300	chr1:223310736-223311104	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr1:223310723-223311194	MCF-7	breast:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
34	CEBPB	chr1:223310648-223311241	ECC-1	luminal epithelium:	n/a	chr1:223310950-223310961 chr1:223310934-223310945

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
2	chr1:223295440..223297086-chr1:223310909..223313590,2	MCF-7	breast:

Variant related genes	Relation type
TLR5	TF binding region
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11485987	1.00[MEX][hapmap]
rs1640806	1.00[MEX][hapmap]
rs1640862	1.00[MEX][hapmap]
rs5744127	1.00[AMR][1000 genomes]
rs5744135	1.00[MEX][hapmap]
rs5744138	1.00[MEX][hapmap]
rs5744139	1.00[MEX][hapmap]
rs5744140	1.00[MEX][hapmap]
rs5744143	1.00[MEX][hapmap]
rs5744149	1.00[MEX][hapmap]
rs851153	1.00[MEX][hapmap]
rs851159	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
4	chr1:223307600-223311600	Enhancers	Placenta	Placenta
5	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
6	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
7	chr1:223307800-223311200	Enhancers	HMEC	breast
8	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:223308800-223314000	Weak transcription	Gastric	stomach
11	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
12	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
15	chr1:223309000-223311600	Enhancers	Fetal Lung	lung
16	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:223309400-223316000	Weak transcription	NHLF	lung
19	chr1:223309600-223314600	Weak transcription	Ovary	ovary
20	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:223309800-223311200	Weak transcription	Fetal Thymus	thymus
22	chr1:223309800-223313000	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:223309800-223313600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:223309800-223314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:223310000-223311400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:223310200-223311200	Enhancers	Osteobl	bone
28	chr1:223310200-223311400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:223310400-223311200	Enhancers	Liver	Liver
31	chr1:223310400-223311200	Enhancers	Stomach Mucosa	stomach
32	chr1:223310400-223311200	Enhancers	NHDF-Ad	bronchial
33	chr1:223310400-223311200	Enhancers	NHEK	skin
34	chr1:223310400-223311600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:223310400-223311600	Enhancers	Brain Anterior Caudate	brain
36	chr1:223310400-223311600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:223310400-223311600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:223310600-223311200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:223310600-223311200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
40	chr1:223310600-223311200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:223310600-223311200	Enhancers	Duodenum Mucosa	Duodenum
42	chr1:223310600-223311400	Enhancers	Fetal Intestine Large	intestine
43	chr1:223310600-223311600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr1:223310600-223311600	Enhancers	Fetal Intestine Small	intestine
45	chr1:223310600-223314000	Weak transcription	Esophagus	oesophagus
46	chr1:223310600-223314000	Weak transcription	Psoas Muscle	Psoas
47	chr1:223310600-223314200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:223310600-223315400	Weak transcription	Lung	lung
49	chr1:223310800-223311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:223310800-223311200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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