Variant report

Variant	rs5744144
Chromosome Location	chr1:223309040-223309041
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	FOS	chr1:223308570-223309050	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:223308590-223309117	MCF10A-Er-Src	breast:	n/a	n/a
3	NFIC	chr1:223308369-223309127	SK-N-SH	brain:	n/a	n/a
4	MYC	chr1:223308564-223309164	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:223307101-223309223	MCF10A-Er-Src	breast:	n/a	n/a

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: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1341985	0.90[EUR][1000 genomes]
rs1418143	0.90[EUR][1000 genomes]
rs1418144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34088950	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744104	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744106	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744107	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744150	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744151	1.00[ASN][1000 genomes]
rs5744156	1.00[EUR][1000 genomes]
rs72743840	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743847	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743860	0.90[EUR][1000 genomes]
rs72743869	0.90[EUR][1000 genomes]
rs72743871	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743874	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72748469	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748471	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748472	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748475	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748482	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988779	0.90[EUR][1000 genomes]

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:55 , 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	chr1:223307600-223309200	Flanking Active TSS	NHEK	skin
6	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
8	chr1:223307600-223311600	Enhancers	Placenta	Placenta
9	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
10	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
11	chr1:223307800-223309400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:223307800-223309400	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr1:223307800-223309400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr1:223307800-223309600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:223307800-223309800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:223307800-223309800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:223307800-223309800	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:223307800-223310400	Weak transcription	Liver	Liver
19	chr1:223307800-223310400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:223307800-223310400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:223307800-223310400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:223307800-223311200	Enhancers	HMEC	breast
23	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:223308000-223309600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:223308000-223311000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:223308200-223309400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:223308200-223309600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr1:223308200-223309800	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:223308400-223310600	Enhancers	Psoas Muscle	Psoas
30	chr1:223308600-223309600	Bivalent Enhancer	Fetal Stomach	stomach
31	chr1:223308600-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:223308600-223309800	Enhancers	Fetal Muscle Leg	muscle
33	chr1:223308600-223309800	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:223308800-223309200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:223308800-223309400	Enhancers	Primary B cells from cord blood	blood
37	chr1:223308800-223309400	Enhancers	NHLF	lung
38	chr1:223308800-223309600	Enhancers	Colon Smooth Muscle	Colon
39	chr1:223308800-223309600	Enhancers	Stomach Smooth Muscle	stomach
40	chr1:223308800-223310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
41	chr1:223308800-223310800	Weak transcription	Hela-S3	cervix
42	chr1:223308800-223314000	Weak transcription	Gastric	stomach
43	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
44	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
47	chr1:223309000-223309200	Enhancers	Primary T cells from cord blood	blood
48	chr1:223309000-223309400	Weak transcription	Ovary	ovary
49	chr1:223309000-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:223309000-223309800	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links