Variant report

Variant	rs1466535
Chromosome Location	chr12:57534470-57534471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57527304..57529324-chr12:57534338..57535887,2	K562	blood:
2	chr12:57532929..57534567-chr12:57561510..57563963,2	K562	blood:
3	chr12:57533511..57536454-chr12:57538764..57541311,2	MCF-7	breast:
4	chr12:57531018..57534803-chr12:57534919..57538004,3	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747776	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876964	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10876965	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11172113	1.00[JPT][hapmap]
rs11172114	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1385526	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4257011	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4367982	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759044	0.84[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs4759045	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759277	1.00[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Abdominal aortic aneurysm	22055160	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1466535	KIF5A	cis	cerebellum	SCAN
rs1466535	STAT6	cis	lymphoblastoid	seeQTL
rs1466535	ATP5B	cis	cerebellum	SCAN
rs1466535	SUOX	cis	cerebellum	SCAN
rs1466535	SNORD59A	cis	cerebellum	SCAN
rs1466535	SMARCC2	cis	cerebellum	SCAN
rs1466535	STAT6	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57523400-57557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:57523800-57537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:57524000-57542200	Weak transcription	HMEC	breast
4	chr12:57524000-57543000	Weak transcription	NHEK	skin
5	chr12:57526200-57534800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:57527000-57534600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:57530000-57537600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:57530400-57538200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:57530600-57535000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:57530600-57536600	Weak transcription	Thymus	Thymus
11	chr12:57530600-57538400	Weak transcription	Fetal Heart	heart
12	chr12:57531200-57534600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:57531200-57535800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:57531200-57536600	Genic enhancers	Muscle Satellite Cultured Cells	--
15	chr12:57531200-57542800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:57531400-57537600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr12:57531600-57536600	Genic enhancers	HSMM	muscle
18	chr12:57531600-57537400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:57531600-57539000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:57531600-57539600	Strong transcription	Brain Germinal Matrix	brain
21	chr12:57531600-57544000	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr12:57531800-57535800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:57531800-57536000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:57531800-57536400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:57531800-57542800	Weak transcription	Psoas Muscle	Psoas
26	chr12:57531800-57544200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:57531800-57545000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:57531800-57545200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:57531800-57576000	Strong transcription	Fetal Brain Female	brain
30	chr12:57532000-57539000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr12:57532000-57540000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:57532000-57540400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:57532000-57540400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:57532200-57535200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr12:57532200-57535200	Genic enhancers	Placenta	Placenta
36	chr12:57532200-57535600	Strong transcription	Colon Smooth Muscle	Colon
37	chr12:57532200-57536200	Strong transcription	Fetal Brain Male	brain
38	chr12:57532200-57536400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:57532200-57537400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:57532200-57541000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:57532200-57544000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:57532400-57535200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:57532400-57537600	Genic enhancers	NHDF-Ad	bronchial
44	chr12:57532400-57539200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:57532400-57540000	Strong transcription	Aorta	Aorta
46	chr12:57532400-57540600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr12:57532400-57541000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr12:57532400-57542600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:57532600-57535400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:57532800-57535000	Strong transcription	Brain Substantia Nigra	brain

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