Variant report

Variant	rs5744147
Chromosome Location	chr1:223308196-223308197
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	STAT3	chr1:223307106-223308348	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:223307047-223308266	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:223307156-223308315	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:223307101-223309223	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:223308033-223308247	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
2	chr1:223305860..223308306-chr1:223535536..223539484,5	MCF-7	breast:
3	chr1:223306168..223308719-chr1:223316086..223318176,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUSD4-2	chr1:223308024-223308206	NONHSAT009730

Variant related genes	Relation type
TLR5	TF binding region
ENSG00000143502	Chromatin interaction
ENSG00000187554	Chromatin interaction
ENSG00000236846	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10489492	0.82[ASN][1000 genomes]
rs1361642	0.84[ASN][1000 genomes]
rs1418145	0.93[ASN][1000 genomes]
rs1418146	0.93[ASN][1000 genomes]
rs1640809	0.82[ASN][1000 genomes]
rs1640811	0.82[ASN][1000 genomes]
rs1640812	0.82[ASN][1000 genomes]
rs1640813	0.82[ASN][1000 genomes]
rs1640814	0.82[ASN][1000 genomes]
rs1640815	0.82[ASN][1000 genomes]
rs1640816	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]
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	0.82[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]
rs45501199	1.00[ASN][1000 genomes]
rs5744135	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744138	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744139	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744140	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744143	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5744149	0.95[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]
rs723961	0.82[ASN][1000 genomes]
rs72743851	0.82[ASN][1000 genomes]
rs759303	0.82[ASN][1000 genomes]
rs763389	0.97[ASN][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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223306600-223308800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:223306600-223308800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:223306600-223310000	Enhancers	Lung	lung
5	chr1:223306800-223308600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:223306800-223310000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223306800-223310600	Enhancers	Esophagus	oesophagus
8	chr1:223307000-223308400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:223307200-223308200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:223307400-223308200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
11	chr1:223307400-223309000	Bivalent Enhancer	Fetal Thymus	thymus
12	chr1:223307600-223308200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
14	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr1:223307600-223308400	Enhancers	Fetal Intestine Large	intestine
17	chr1:223307600-223308400	Weak transcription	Ovary	ovary
18	chr1:223307600-223308400	Weak transcription	Psoas Muscle	Psoas
19	chr1:223307600-223308800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:223307600-223308800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:223307600-223308800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:223307600-223308800	Enhancers	Stomach Mucosa	stomach
23	chr1:223307600-223309200	Flanking Active TSS	NHEK	skin
24	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
26	chr1:223307600-223311600	Enhancers	Placenta	Placenta
27	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
28	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
29	chr1:223307800-223308200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:223307800-223308200	Bivalent Enhancer	Primary T cells from cord blood	blood
31	chr1:223307800-223308200	Weak transcription	Colonic Mucosa	Colon
32	chr1:223307800-223308200	Bivalent Enhancer	Fetal Kidney	kidney
33	chr1:223307800-223308200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:223307800-223308200	Enhancers	Fetal Muscle Leg	muscle
35	chr1:223307800-223308400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:223307800-223308400	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr1:223307800-223308400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:223307800-223308600	Weak transcription	Aorta	Aorta
39	chr1:223307800-223308600	Enhancers	Colon Smooth Muscle	Colon
40	chr1:223307800-223308600	Enhancers	NH-A	brain
41	chr1:223307800-223308600	Bivalent Enhancer	Osteobl	bone
42	chr1:223307800-223308800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:223307800-223308800	Enhancers	Pancreas	Pancrea
44	chr1:223307800-223308800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr1:223307800-223308800	Enhancers	Hela-S3	cervix
46	chr1:223307800-223309000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:223307800-223309000	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:223307800-223309000	Bivalent Enhancer	Fetal Lung	lung
49	chr1:223307800-223309000	Enhancers	HSMM	muscle
50	chr1:223307800-223309000	Enhancers	NHDF-Ad	bronchial

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