Variant report

Variant	rs12455909
Chromosome Location	chr18:12599511-12599512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12598216..12599917-chr18:12611119..12613294,2	MCF-7	breast:
2	chr18:12548166..12550496-chr18:12597358..12599512,2	MCF-7	breast:

Extended variants
information (count: 153 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10401097	0.93[ASN][1000 genomes]
rs10445428	0.85[ASN][1000 genomes]
rs11080582	0.85[ASN][1000 genomes]
rs11080583	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080584	0.86[ASN][1000 genomes]
rs11080585	0.93[ASN][1000 genomes]
rs11080586	0.94[ASN][1000 genomes]
rs11080590	0.92[ASN][1000 genomes]
rs11659510	0.84[ASN][1000 genomes]
rs11659854	0.94[ASN][1000 genomes]
rs11663958	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	0.92[AFR][1000 genomes]
rs12454931	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12455093	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455536	0.84[ASN][1000 genomes]
rs12455892	0.89[ASN][1000 genomes]
rs12457903	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604184	0.93[ASN][1000 genomes]
rs12604385	0.96[ASN][1000 genomes]
rs12604400	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12604402	0.81[ASN][1000 genomes]
rs12604541	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12605240	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12605392	0.92[ASN][1000 genomes]
rs12606465	0.83[ASN][1000 genomes]
rs12606506	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709540	0.85[ASN][1000 genomes]
rs12953406	0.85[ASN][1000 genomes]
rs12953578	0.93[ASN][1000 genomes]
rs12954614	0.94[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	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12959015	0.85[AMR][1000 genomes];0.96[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]
rs12962476	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963179	0.91[ASN][1000 genomes]
rs12963325	0.91[ASN][1000 genomes]
rs12964660	0.83[ASN][1000 genomes]
rs12965094	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12969567	0.88[ASN][1000 genomes]
rs12970025	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12970174	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1893193	0.94[ASN][1000 genomes]
rs1940974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1940975	0.94[ASN][1000 genomes]
rs2155698	0.94[ASN][1000 genomes]
rs2186907	0.94[ASN][1000 genomes]
rs28414067	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28457089	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28496036	0.96[ASN][1000 genomes]
rs28582228	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647784	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28886423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072260	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34178879	0.85[ASN][1000 genomes]
rs34438212	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34456643	0.86[ASN][1000 genomes]
rs34814556	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34899007	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35122110	0.87[ASN][1000 genomes]
rs35449211	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35630805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35963756	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4389196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493131	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4627434	0.94[ASN][1000 genomes]
rs4629035	0.93[ASN][1000 genomes]
rs55749182	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58215411	0.84[ASN][1000 genomes]
rs60505421	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62097094	0.83[ASN][1000 genomes]
rs62097102	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62097103	0.88[ASN][1000 genomes]
rs62097126	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62097148	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62097149	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62097152	0.92[ASN][1000 genomes]
rs62097153	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67045810	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67268432	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs70964152	0.83[ASN][1000 genomes]
rs722708	0.84[ASN][1000 genomes]
rs7234697	0.91[ASN][1000 genomes]
rs7237732	0.89[ASN][1000 genomes]
rs7238080	0.91[ASN][1000 genomes]
rs723836	0.84[ASN][1000 genomes]
rs7238546	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7242395	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7504857	0.92[ASN][1000 genomes]
rs755020	0.92[ASN][1000 genomes]
rs755021	0.92[ASN][1000 genomes]
rs8086094	0.92[ASN][1000 genomes]
rs8087885	0.87[ASN][1000 genomes]
rs8088786	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8089081	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8089115	0.91[ASN][1000 genomes]
rs8089619	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8093129	0.92[ASN][1000 genomes]
rs8093532	0.87[ASN][1000 genomes]
rs8093571	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095160	0.94[ASN][1000 genomes]
rs8096455	0.93[ASN][1000 genomes]
rs9303772	0.93[ASN][1000 genomes]
rs9303773	0.93[ASN][1000 genomes]
rs948301	0.92[ASN][1000 genomes]
rs948302	0.92[ASN][1000 genomes]
rs948303	0.83[ASN][1000 genomes]
rs9675543	0.92[ASN][1000 genomes]
rs9710023	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9945339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9945374	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9947738	0.92[ASN][1000 genomes]
rs9948505	0.93[ASN][1000 genomes]
rs9948618	0.91[ASN][1000 genomes]
rs9949582	0.87[ASN][1000 genomes]
rs9951147	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9954054	0.93[ASN][1000 genomes]
rs9954419	0.88[ASN][1000 genomes]
rs9958409	0.93[ASN][1000 genomes]
rs9958666	0.88[ASN][1000 genomes]
rs9959191	0.83[AFR][1000 genomes]
rs9959759	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9960824	0.92[ASN][1000 genomes]
rs9961705	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9961851	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9964759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9965123	0.93[ASN][1000 genomes]
rs9989496	0.92[ASN][1000 genomes]
rs9989506	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
rs12455909	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs12455909	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12594600-12600400	Enhancers	HepG2	liver
2	chr18:12595400-12600400	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr18:12595600-12600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:12595600-12600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr18:12595600-12600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr18:12595800-12600600	Enhancers	HMEC	breast
7	chr18:12596000-12599600	Enhancers	Fetal Kidney	kidney
8	chr18:12596600-12600000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr18:12596800-12599600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12596800-12599800	Enhancers	Fetal Brain Female	brain
11	chr18:12596800-12600400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:12596800-12600400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr18:12596800-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:12596800-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:12596800-12600600	Enhancers	NHDF-Ad	bronchial
16	chr18:12596800-12600600	Enhancers	NHEK	skin
17	chr18:12597000-12599600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:12597000-12600200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr18:12597000-12605800	Weak transcription	Gastric	stomach
20	chr18:12597000-12605800	Weak transcription	K562	blood
21	chr18:12597000-12606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr18:12597200-12600000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr18:12597200-12600400	Enhancers	NHLF	lung
24	chr18:12597400-12599800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr18:12597400-12600400	Enhancers	Primary T cells from cord blood	blood
26	chr18:12597600-12600400	Enhancers	HSMM	muscle
27	chr18:12597800-12610800	Weak transcription	Right Ventricle	heart
28	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
29	chr18:12598000-12600000	Enhancers	A549	lung
30	chr18:12598000-12600400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:12598000-12600400	Enhancers	Osteobl	bone
32	chr18:12598000-12600600	Enhancers	HSMMtube	muscle
33	chr18:12598000-12601800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr18:12598000-12601800	Weak transcription	Brain Hippocampus Middle	brain
35	chr18:12598000-12601800	Weak transcription	Fetal Thymus	thymus
36	chr18:12598000-12606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr18:12598000-12607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:12598000-12607200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr18:12598000-12610000	Weak transcription	Lung	lung
40	chr18:12598200-12600400	Enhancers	Primary hematopoietic stem cells	blood
41	chr18:12598200-12606800	Weak transcription	Brain Anterior Caudate	brain
42	chr18:12598600-12600000	Enhancers	Pancreas	Pancrea
43	chr18:12598600-12608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr18:12598800-12599600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr18:12598800-12599800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:12598800-12600400	Enhancers	Hela-S3	cervix
47	chr18:12598800-12600400	Enhancers	HUVEC	blood vessel
48	chr18:12598800-12600600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr18:12598800-12606000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr18:12598800-12606000	Weak transcription	Left Ventricle	heart

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