Variant report

Variant	rs28821540
Chromosome Location	chr18:12558308-12558309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10048276	0.87[ASN][1000 genomes]
rs1105122	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11660232	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11662531	0.87[ASN][1000 genomes]
rs11663289	0.84[EUR][1000 genomes]
rs11663358	1.00[ASN][1000 genomes]
rs11663668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11664013	0.87[ASN][1000 genomes]
rs11664068	0.87[ASN][1000 genomes]
rs11664219	1.00[ASN][1000 genomes]
rs11664431	0.81[EUR][1000 genomes]
rs11664773	1.00[ASN][1000 genomes]
rs11665415	1.00[ASN][1000 genomes]
rs11665542	1.00[ASN][1000 genomes]
rs1592641	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17595746	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1940973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155699	1.00[ASN][1000 genomes]
rs2186906	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527375	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565322	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28575715	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634564	0.87[ASN][1000 genomes]
rs28663159	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28801690	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28815517	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029848	1.00[ASN][1000 genomes]
rs56870830	1.00[ASN][1000 genomes]
rs57706356	1.00[ASN][1000 genomes]
rs58638386	1.00[ASN][1000 genomes]
rs60563648	1.00[ASN][1000 genomes]
rs61027502	0.87[ASN][1000 genomes]
rs73405602	1.00[ASN][1000 genomes]
rs73407510	1.00[ASN][1000 genomes]
rs73407511	1.00[ASN][1000 genomes]
rs73407524	1.00[ASN][1000 genomes]
rs9946557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959201	1.00[ASN][1000 genomes]
rs9960604	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9960706	0.87[ASN][1000 genomes]
rs9963755	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9966118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967026	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12552400-12559600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr18:12552400-12560000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:12553200-12559600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12553600-12567600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr18:12553600-12574600	Weak transcription	Right Ventricle	heart
6	chr18:12553800-12560000	Weak transcription	Left Ventricle	heart
7	chr18:12553800-12569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:12554200-12567600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr18:12555200-12559400	Weak transcription	Aorta	Aorta
10	chr18:12556800-12558600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:12557000-12559600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:12557000-12559800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:12557000-12559800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr18:12557000-12560000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr18:12557200-12558400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:12557200-12558400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr18:12557200-12559200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr18:12557600-12559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr18:12557600-12559600	Weak transcription	Esophagus	oesophagus
20	chr18:12557600-12580800	Weak transcription	Pancreas	Pancrea
21	chr18:12557800-12558400	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr18:12557800-12558400	ZNF genes & repeats	Fetal Brain Female	brain
23	chr18:12557800-12558400	ZNF genes & repeats	Fetal Lung	lung
24	chr18:12558000-12558400	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr18:12558000-12558400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
26	chr18:12558000-12558800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:12558000-12559200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:12558000-12559600	ZNF genes & repeats	Fetal Stomach	stomach
29	chr18:12558200-12559400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr18:12558200-12559600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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