Variant report

Variant	rs12962476
Chromosome Location	chr18:12607210-12607211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12595958..12597985-chr18:12607168..12608800,2	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
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10401097	0.93[ASN][1000 genomes]
rs10445428	0.85[ASN][1000 genomes]
rs11080582	0.85[ASN][1000 genomes]
rs11080583	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080584	0.86[ASN][1000 genomes]
rs11080585	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11080586	0.94[ASN][1000 genomes]
rs11080590	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11659510	0.84[ASN][1000 genomes]
rs11659854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11663958	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11664404	0.91[ASN][1000 genomes]
rs11664765	0.93[ASN][1000 genomes]
rs11664861	0.92[ASN][1000 genomes]
rs11664914	0.92[ASN][1000 genomes]
rs11664917	0.92[ASN][1000 genomes]
rs11664927	0.87[ASN][1000 genomes]
rs11664936	0.90[ASN][1000 genomes]
rs11665543	0.94[ASN][1000 genomes]
rs12326271	0.94[ASN][1000 genomes]
rs12454322	0.90[AFR][1000 genomes]
rs12454931	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12455093	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455536	0.84[ASN][1000 genomes]
rs12455892	0.89[ASN][1000 genomes]
rs12455909	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604184	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12604385	0.96[ASN][1000 genomes]
rs12604400	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12604402	0.81[ASN][1000 genomes]
rs12604541	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12605240	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12605392	0.92[ASN][1000 genomes]
rs12606465	0.83[ASN][1000 genomes]
rs12606506	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709540	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12953406	0.85[ASN][1000 genomes]
rs12953578	0.93[ASN][1000 genomes]
rs12954614	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12955161	0.83[ASN][1000 genomes]
rs12955490	0.82[ASN][1000 genomes]
rs12956133	0.93[ASN][1000 genomes]
rs12956385	0.83[ASN][1000 genomes]
rs12956885	0.92[ASN][1000 genomes]
rs12957048	0.91[ASN][1000 genomes]
rs12957151	0.88[ASN][1000 genomes]
rs12957688	0.91[ASN][1000 genomes]
rs12958200	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12959015	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12960150	0.93[ASN][1000 genomes]
rs12961695	0.84[ASN][1000 genomes]
rs12961966	0.85[ASN][1000 genomes]
rs12963179	0.91[ASN][1000 genomes]
rs12963325	0.91[ASN][1000 genomes]
rs12964660	0.83[ASN][1000 genomes]
rs12965094	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12969567	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12970025	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12970174	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17615158	0.82[CEU][hapmap]
rs1864532	0.83[JPT][hapmap]
rs1893193	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1940974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1940975	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2155698	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2186907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28414067	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28457089	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28496036	0.96[ASN][1000 genomes]
rs28582228	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647784	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28886423	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072260	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34178879	0.85[ASN][1000 genomes]
rs34438212	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34456643	0.86[ASN][1000 genomes]
rs34814556	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34899007	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35122110	0.87[ASN][1000 genomes]
rs35449211	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35630805	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35963756	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4389196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493131	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4627434	0.94[ASN][1000 genomes]
rs4629035	0.93[ASN][1000 genomes]
rs55749182	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58215411	0.84[ASN][1000 genomes]
rs60505421	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62097094	0.83[ASN][1000 genomes]
rs62097102	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62097103	0.88[ASN][1000 genomes]
rs62097126	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62097148	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62097149	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62097152	0.92[ASN][1000 genomes]
rs62097153	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67045810	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67268432	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs70964152	0.83[ASN][1000 genomes]
rs722708	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7234697	0.91[ASN][1000 genomes]
rs7237732	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7238080	0.91[ASN][1000 genomes]
rs723836	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7238546	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7242395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7504857	0.92[ASN][1000 genomes]
rs755020	0.92[ASN][1000 genomes]
rs755021	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8086094	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8087885	0.87[ASN][1000 genomes]
rs8088786	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8089081	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8089115	0.91[ASN][1000 genomes]
rs8089619	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8093129	0.92[ASN][1000 genomes]
rs8093532	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8093571	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095160	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs8096455	0.93[ASN][1000 genomes]
rs9303772	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9303773	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9303774	0.95[YRI][hapmap]
rs948301	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs948302	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs948303	0.83[ASN][1000 genomes]
rs9675543	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9710023	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9945339	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9945374	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9947738	0.92[ASN][1000 genomes]
rs9948505	0.93[ASN][1000 genomes]
rs9948618	0.91[ASN][1000 genomes]
rs9949582	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9951147	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9954054	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9954419	0.88[ASN][1000 genomes]
rs9958409	0.93[ASN][1000 genomes]
rs9958666	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9959191	0.81[AFR][1000 genomes]
rs9959759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9960824	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9961705	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9961851	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9964759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9965123	0.93[ASN][1000 genomes]
rs9989496	0.92[ASN][1000 genomes]
rs9989506	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9989568	0.93[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12962476	SPIRE1	cis	Muscle Skeletal	GTEx
rs12962476	RP11-861E21.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12597800-12610800	Weak transcription	Right Ventricle	heart
2	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
3	chr18:12598000-12610000	Weak transcription	Lung	lung
4	chr18:12598600-12608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr18:12598800-12609000	Weak transcription	Right Atrium	heart
6	chr18:12600000-12607400	Weak transcription	Pancreas	Pancrea
7	chr18:12600400-12608600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:12602200-12609200	Weak transcription	Fetal Brain Male	brain
9	chr18:12602200-12638400	Weak transcription	Fetal Brain Female	brain
10	chr18:12602800-12611200	Weak transcription	Spleen	Spleen
11	chr18:12604800-12610800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr18:12605600-12608200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr18:12605800-12607800	Enhancers	Primary hematopoietic stem cells	blood
14	chr18:12605800-12608200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:12605800-12609200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr18:12605800-12609600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:12605800-12609800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr18:12606000-12607400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:12606000-12608000	Enhancers	Left Ventricle	heart
20	chr18:12606000-12608200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr18:12606000-12610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:12606000-12615600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12606200-12607400	Weak transcription	Esophagus	oesophagus
24	chr18:12606200-12610000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr18:12606200-12616200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr18:12606400-12607400	Enhancers	HSMMtube	muscle
27	chr18:12606400-12607600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:12606400-12607800	Enhancers	K562	blood
29	chr18:12606400-12609400	Enhancers	Osteobl	bone
30	chr18:12606400-12609600	Enhancers	HMEC	breast
31	chr18:12606600-12608800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:12606600-12609200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:12606600-12611600	Enhancers	HepG2	liver
34	chr18:12606800-12607400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr18:12606800-12607400	Enhancers	NHDF-Ad	bronchial
36	chr18:12606800-12607600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr18:12606800-12607600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr18:12606800-12607800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:12606800-12607800	Flanking Active TSS	Hela-S3	cervix
40	chr18:12606800-12608000	Enhancers	Brain Cingulate Gyrus	brain
41	chr18:12606800-12609000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:12606800-12609000	Enhancers	HSMM	muscle
43	chr18:12606800-12609200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr18:12606800-12609200	Enhancers	Brain Anterior Caudate	brain
45	chr18:12606800-12609400	Enhancers	Brain Hippocampus Middle	brain
46	chr18:12607000-12607600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr18:12607000-12607600	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr18:12607000-12607800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:12607000-12607800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr18:12607000-12607800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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