Variant report

Variant	rs5744140
Chromosome Location	chr1:223309533-223309534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223309500-223309650	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr1:223309405-223309846	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:223309492-223309815	K562	blood:	n/a	n/a
4	CTCF	chr1:223309500-223309650	GM12871	blood:	n/a	n/a
5	CTCF	chr1:223309460-223309610	BE2_C	brain:	n/a	n/a
6	CTCF	chr1:223309520-223309670	GM12869	blood:	n/a	n/a
7	CTCF	chr1:223309433-223309838	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr1:223309508-223309845	MCF-7	breast:	n/a	n/a
9	RAD21	chr1:223309531-223309955	HCT-116	colon:	n/a	n/a
10	ZNF143	chr1:223309486-223309761	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr1:223309491-223309760	HepG2	liver:	n/a	n/a
12	RAD21	chr1:223309508-223309818	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr1:223309483-223309815	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr1:223309500-223309650	SAEC	small airway:	n/a	n/a
15	CTCF	chr1:223309460-223309610	HAc	cerebellar:	n/a	n/a
16	RAD21	chr1:223309492-223309744	GM12878	blood:	n/a	n/a
17	CTCF	chr1:223309475-223309830	GM12878	blood:	n/a	n/a
18	CTCF	chr1:223309474-223309826	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
2	chr1:223309399..223310109-chr1:223871653..223872525,2	K562	blood:

No data

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]
rs5744135	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]
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];0.87[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];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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223306600-223310000	Enhancers	Lung	lung
3	chr1:223306800-223310000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223306800-223310600	Enhancers	Esophagus	oesophagus
5	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
7	chr1:223307600-223311600	Enhancers	Placenta	Placenta
8	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
9	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
10	chr1:223307800-223309600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:223307800-223309800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:223307800-223309800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:223307800-223309800	Enhancers	Rectal Smooth Muscle	rectum
14	chr1:223307800-223310400	Weak transcription	Liver	Liver
15	chr1:223307800-223310400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:223307800-223310400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:223307800-223310400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:223307800-223311200	Enhancers	HMEC	breast
19	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:223308000-223309600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:223308000-223311000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:223308200-223309600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr1:223308200-223309800	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:223308400-223310600	Enhancers	Psoas Muscle	Psoas
25	chr1:223308600-223309600	Bivalent Enhancer	Fetal Stomach	stomach
26	chr1:223308600-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:223308600-223309800	Enhancers	Fetal Muscle Leg	muscle
28	chr1:223308600-223309800	Genic enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:223308800-223309600	Enhancers	Colon Smooth Muscle	Colon
31	chr1:223308800-223309600	Enhancers	Stomach Smooth Muscle	stomach
32	chr1:223308800-223310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
33	chr1:223308800-223310800	Weak transcription	Hela-S3	cervix
34	chr1:223308800-223314000	Weak transcription	Gastric	stomach
35	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
36	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
39	chr1:223309000-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:223309000-223309800	Enhancers	Osteobl	bone
41	chr1:223309000-223310400	Weak transcription	NHDF-Ad	bronchial
42	chr1:223309000-223310600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:223309000-223310600	Weak transcription	HSMM	muscle
44	chr1:223309000-223311600	Enhancers	Fetal Lung	lung
45	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:223309200-223309600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:223309200-223309600	Bivalent Enhancer	Fetal Thymus	thymus
48	chr1:223309200-223310000	Enhancers	NHEK	skin
49	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
50	chr1:223309400-223309600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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