Variant report

Variant	rs5744135
Chromosome Location	chr1:223310618-223310619
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	chr1:223310596-223311257	MCF-7	breast:	n/a	chr1:223310950-223310961 chr1:223310934-223310945
2	CEBPB	chr1:223310567-223311249	HCT-116	colon:	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:

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

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10489492	0.82[ASN][1000 genomes]
rs11485987	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1361642	0.84[ASN][1000 genomes]
rs1418145	0.93[ASN][1000 genomes]
rs1418146	0.93[ASN][1000 genomes]
rs1640803	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs1640806	1.00[MEX][hapmap]
rs1640809	0.82[ASN][1000 genomes]
rs1640811	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs1640812	0.82[ASN][1000 genomes]
rs1640813	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs1640814	0.82[ASN][1000 genomes]
rs1640815	0.82[ASN][1000 genomes]
rs1640816	0.82[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs1640817	0.84[ASN][1000 genomes]
rs1640818	0.84[ASN][1000 genomes]
rs1640819	0.84[ASN][1000 genomes]
rs1640820	0.86[ASN][1000 genomes]
rs1640823	0.84[ASN][1000 genomes]
rs1640862	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs1773738	0.82[ASN][1000 genomes]
rs1773744	0.82[ASN][1000 genomes]
rs1773761	0.82[ASN][1000 genomes]
rs1773762	0.82[ASN][1000 genomes]
rs1773763	0.82[ASN][1000 genomes]
rs1773765	0.82[ASN][1000 genomes]
rs1773766	0.84[ASN][1000 genomes]
rs1773767	0.84[ASN][1000 genomes]
rs1773768	0.84[ASN][1000 genomes]
rs1935305	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs2241095	1.00[ASN][1000 genomes]
rs2256707	0.82[ASN][1000 genomes]
rs2302597	0.86[ASN][1000 genomes]
rs2430400	0.82[ASN][1000 genomes]
rs2487834	0.82[ASN][1000 genomes]
rs2487836	0.82[ASN][1000 genomes]
rs34136554	0.82[ASN][1000 genomes]
rs3768284	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs45501199	1.00[ASN][1000 genomes]
rs5744134	1.00[MEX][hapmap]
rs5744138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744139	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744140	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744143	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744147	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744149	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744156	0.87[ASN][1000 genomes]
rs66662427	0.82[ASN][1000 genomes]
rs66757010	0.82[ASN][1000 genomes]
rs66832195	0.82[ASN][1000 genomes]
rs67573944	0.82[ASN][1000 genomes]
rs712862	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs723961	0.82[ASN][1000 genomes]
rs72743851	0.82[ASN][1000 genomes]
rs759303	0.82[ASN][1000 genomes]
rs763389	0.97[ASN][1000 genomes]
rs851140	1.00[JPT][hapmap]
rs851148	1.00[ASW][hapmap]
rs851151	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs851152	1.00[ASW][hapmap]
rs851153	1.00[MEX][hapmap]
rs851159	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs851211	1.00[JPT][hapmap]
rs851215	1.00[JPT][hapmap]
rs860372	1.00[JPT][hapmap]
rs988241	0.95[CHD][hapmap]
rs988242	0.95[CHD][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:57 , 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	chr1:223308000-223311000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:223308800-223310800	Weak transcription	Hela-S3	cervix
12	chr1:223308800-223314000	Weak transcription	Gastric	stomach
13	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
14	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
17	chr1:223309000-223311600	Enhancers	Fetal Lung	lung
18	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
20	chr1:223309400-223316000	Weak transcription	NHLF	lung
21	chr1:223309600-223314600	Weak transcription	Ovary	ovary
22	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:223309800-223310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:223309800-223310800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:223309800-223311200	Weak transcription	Fetal Thymus	thymus
26	chr1:223309800-223313000	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:223309800-223313600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:223309800-223314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:223310000-223311400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:223310200-223311200	Enhancers	Osteobl	bone
32	chr1:223310200-223311400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:223310400-223310800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:223310400-223310800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr1:223310400-223311200	Enhancers	Liver	Liver
37	chr1:223310400-223311200	Enhancers	Stomach Mucosa	stomach
38	chr1:223310400-223311200	Enhancers	NHDF-Ad	bronchial
39	chr1:223310400-223311200	Enhancers	NHEK	skin
40	chr1:223310400-223311600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:223310400-223311600	Enhancers	Brain Anterior Caudate	brain
42	chr1:223310400-223311600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:223310400-223311600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr1:223310600-223310800	Enhancers	HSMM	muscle
45	chr1:223310600-223311000	Active TSS	Primary hematopoietic stem cells	blood
46	chr1:223310600-223311000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
47	chr1:223310600-223311200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:223310600-223311200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
49	chr1:223310600-223311200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:223310600-223311200	Enhancers	Duodenum Mucosa	Duodenum

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