Variant report

Variant	rs571690
Chromosome Location	chr18:43414078-43414079
allele	G/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	POLR2A	chr18:43413590-43414494	U87	brain:	n/a	n/a
2	POLR2A	chr18:43414047-43414443	U87	brain:	n/a	n/a
3	POLR2A	chr18:43413704-43414443	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:43371899..43373574-chr18:43414036..43416865,2	MCF-7	breast:
2	chr18:43404473..43406777-chr18:43413212..43415646,2	MCF-7	breast:
3	chr18:43408715..43411346-chr18:43413639..43417024,3	MCF-7	breast:

Variant related genes	Relation type
SIGLEC15	TF binding region
ENSG00000197046	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1055066	0.87[CEU][hapmap];0.87[CHD][hapmap]
rs10853537	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs11082489	1.00[MEX][hapmap]
rs11082490	0.87[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs11082491	0.81[ASN][1000 genomes]
rs11661333	0.87[CEU][hapmap]
rs12458195	0.87[CEU][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap]
rs12604912	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1371976	0.87[CEU][hapmap]
rs1660561	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1790299	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1893523	0.87[CEU][hapmap]
rs2919643	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2958437	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35316177	0.86[ASN][1000 genomes]
rs492411	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs500899	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs507653	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs570975	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61104666	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7233909	0.91[CEU][hapmap]
rs8085782	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8099496	0.87[CEU][hapmap]
rs9950673	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525268	chr18:42748365-43474795	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43408400-43415400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr18:43408400-43417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:43408800-43414600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:43408800-43416400	Enhancers	Fetal Intestine Small	intestine
5	chr18:43409400-43414600	Weak transcription	Liver	Liver
6	chr18:43409400-43415400	Weak transcription	Colon Smooth Muscle	Colon
7	chr18:43409400-43418000	Weak transcription	NHDF-Ad	bronchial
8	chr18:43409800-43414200	Weak transcription	HMEC	breast
9	chr18:43409800-43414600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr18:43409800-43416600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:43409800-43417400	Weak transcription	Pancreas	Pancrea
12	chr18:43410200-43414200	Weak transcription	Thymus	Thymus
13	chr18:43410200-43414400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:43410200-43414400	Weak transcription	Small Intestine	intestine
15	chr18:43410400-43414200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr18:43410400-43414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:43410400-43417400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr18:43412000-43417400	Enhancers	Duodenum Mucosa	Duodenum
19	chr18:43412000-43418000	Enhancers	Stomach Mucosa	stomach
20	chr18:43412600-43416600	Enhancers	Fetal Intestine Large	intestine
21	chr18:43412600-43417400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr18:43412800-43420000	Enhancers	Primary hematopoietic stem cells	blood
23	chr18:43413000-43419600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr18:43413200-43414400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:43413200-43414400	Weak transcription	Osteobl	bone
26	chr18:43413200-43417000	Weak transcription	NH-A	brain
27	chr18:43413400-43416200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr18:43414000-43414200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:43414000-43414200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr18:43414000-43414200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr18:43414000-43414400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr18:43414000-43414400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr18:43414000-43414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:43414000-43414800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:43414000-43415000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr18:43414000-43415000	Enhancers	Gastric	stomach
37	chr18:43414000-43415800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr18:43414000-43417200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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