Variant report

Variant	rs2053825
Chromosome Location	chr18:29114149-29114150
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29112621..29114426-chr18:29114667..29118167,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10163532	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10502573	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11542765	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12327220	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12604517	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12605787	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12607843	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12607944	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375443	0.93[EUR][1000 genomes]
rs16962075	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16962077	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17802774	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1791155	0.90[EUR][1000 genomes]
rs2053826	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053827	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096918	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2256638	0.92[EUR][1000 genomes]
rs2278792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290128	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290129	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28376849	0.80[ASN][1000 genomes]
rs3737375	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3737378	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3829628	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470222	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471764	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55899143	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56389431	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62095191	0.91[EUR][1000 genomes]
rs62095194	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62095195	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62095196	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62095222	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095223	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095226	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7244098	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7506013	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9807377	0.88[EUR][1000 genomes]
rs9807379	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29092000-29115600	Weak transcription	GM12878-XiMat	blood
2	chr18:29094000-29118800	Weak transcription	Gastric	stomach
3	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
4	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr18:29097000-29116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:29097000-29118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:29097200-29118400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
10	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr18:29098000-29115400	Weak transcription	Fetal Stomach	stomach
13	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
20	chr18:29101800-29116000	Weak transcription	A549	lung
21	chr18:29102000-29116000	Weak transcription	Placenta	Placenta
22	chr18:29102400-29116000	Weak transcription	Fetal Lung	lung
23	chr18:29102400-29118400	Weak transcription	Thymus	Thymus
24	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:29103800-29114200	Weak transcription	Primary T cells from cord blood	blood
26	chr18:29104000-29116200	Weak transcription	Fetal Kidney	kidney
27	chr18:29104200-29118400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr18:29105200-29127600	Weak transcription	Fetal Heart	heart
29	chr18:29105400-29116200	Weak transcription	Left Ventricle	heart
30	chr18:29105400-29119200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:29105400-29119200	Weak transcription	Pancreas	Pancrea
32	chr18:29105400-29120200	Weak transcription	Colonic Mucosa	Colon
33	chr18:29105600-29116200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr18:29105800-29116200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr18:29106600-29116200	Weak transcription	Adipose Nuclei	Adipose
36	chr18:29106800-29116600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:29107200-29120800	Weak transcription	NH-A	brain
38	chr18:29108400-29116800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr18:29108400-29119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr18:29108800-29114200	Weak transcription	NHEK	skin
41	chr18:29110600-29121800	Strong transcription	Hela-S3	cervix
42	chr18:29110800-29123200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:29111000-29127200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr18:29111000-29127400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr18:29111800-29116200	Weak transcription	Liver	Liver
46	chr18:29112000-29116200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr18:29112200-29114800	Weak transcription	Fetal Intestine Large	intestine
48	chr18:29112200-29114800	Weak transcription	K562	blood
49	chr18:29112200-29116000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr18:29112400-29115600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links