Variant report

Variant	rs9959145
Chromosome Location	chr18:12606463-12606464
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12604320..12607057-chr18:12650653..12653511,2	MCF-7	breast:
2	chr18:12596844..12599084-chr18:12603896..12607483,3	K562	blood:
3	chr18:12601083..12604521-chr18:12605372..12609062,5	MCF-7	breast:
4	chr18:12604800..12607453-chr18:12610712..12612678,2	MCF-7	breast:
5	chr18:12604251..12607235-chr18:12656696..12659303,2	MCF-7	breast:
6	chr18:12601660..12604327-chr18:12604536..12607212,2	K562	blood:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10048276	0.87[ASN][1000 genomes]
rs1105122	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11660232	0.83[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11662531	0.87[ASN][1000 genomes]
rs11663289	0.90[EUR][1000 genomes]
rs11663358	1.00[ASN][1000 genomes]
rs11663668	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11664013	0.91[GIH][hapmap];0.87[ASN][1000 genomes]
rs11664068	0.87[ASN][1000 genomes]
rs11664219	1.00[ASN][1000 genomes]
rs11664431	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11664773	1.00[ASN][1000 genomes]
rs11665415	1.00[ASN][1000 genomes]
rs11665542	1.00[ASN][1000 genomes]
rs1592641	0.83[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17595746	0.83[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1940973	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155699	1.00[ASN][1000 genomes]
rs2186906	0.83[CEU][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527375	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28575715	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634564	0.87[ASN][1000 genomes]
rs28663159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28801690	0.85[EUR][1000 genomes]
rs28815517	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821540	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[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	0.83[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947085	1.00[YRI][hapmap]
rs9953831	1.00[YRI][hapmap]
rs9959201	1.00[ASN][1000 genomes]
rs9960604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9960706	0.87[ASN][1000 genomes]
rs9963394	1.00[YRI][hapmap]
rs9963755	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9966118	0.83[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967026	0.83[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989546	0.83[CEU][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

Variant related diseases (count:1)

Disease	PMID	Source
Immune response to smallpox vaccine (IL-6)	22542470	GWAS catalog

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12597000-12606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr18:12597800-12610800	Weak transcription	Right Ventricle	heart
3	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
4	chr18:12598000-12606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:12598000-12607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:12598000-12607200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:12598000-12610000	Weak transcription	Lung	lung
8	chr18:12598200-12606800	Weak transcription	Brain Anterior Caudate	brain
9	chr18:12598600-12608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:12598800-12606800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr18:12598800-12607000	Weak transcription	Brain Angular Gyrus	brain
12	chr18:12598800-12609000	Weak transcription	Right Atrium	heart
13	chr18:12599000-12606800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr18:12599000-12606800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr18:12599800-12607000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr18:12600000-12607400	Weak transcription	Pancreas	Pancrea
17	chr18:12600200-12607000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12600400-12606600	Weak transcription	HepG2	liver
19	chr18:12600400-12606800	Weak transcription	HSMM	muscle
20	chr18:12600400-12607000	Weak transcription	NHLF	lung
21	chr18:12600400-12608600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:12600600-12606800	Weak transcription	NHDF-Ad	bronchial
23	chr18:12602200-12609200	Weak transcription	Fetal Brain Male	brain
24	chr18:12602200-12638400	Weak transcription	Fetal Brain Female	brain
25	chr18:12602600-12606800	Weak transcription	Adipose Nuclei	Adipose
26	chr18:12602800-12611200	Weak transcription	Spleen	Spleen
27	chr18:12603000-12607000	Weak transcription	Fetal Heart	heart
28	chr18:12603200-12606800	Weak transcription	Brain Hippocampus Middle	brain
29	chr18:12604600-12607000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:12604800-12610800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:12605000-12606800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr18:12605200-12606800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:12605600-12608200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr18:12605800-12606800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:12605800-12606800	Enhancers	Hela-S3	cervix
36	chr18:12605800-12607200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:12605800-12607200	Enhancers	HUVEC	blood vessel
38	chr18:12605800-12607800	Enhancers	Primary hematopoietic stem cells	blood
39	chr18:12605800-12608200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr18:12605800-12609200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr18:12605800-12609600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr18:12605800-12609800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr18:12606000-12606600	Weak transcription	Gastric	stomach
44	chr18:12606000-12607200	Enhancers	Stomach Mucosa	stomach
45	chr18:12606000-12607200	Enhancers	NHEK	skin
46	chr18:12606000-12607400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr18:12606000-12608000	Enhancers	Left Ventricle	heart
48	chr18:12606000-12608200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr18:12606000-12610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr18:12606000-12615600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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