Variant report

Variant	rs12457903
Chromosome Location	chr18:12547561-12547562
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	chr18:12511013..12513925-chr18:12546965..12549952,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10445428	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11080582	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11080583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11080584	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11080585	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11080590	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11659854	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11663958	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs11664861	0.81[ASN][1000 genomes]
rs11664914	0.81[ASN][1000 genomes]
rs11664917	0.81[ASN][1000 genomes]
rs12454931	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12455093	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455481	0.81[CEU][hapmap]
rs12455536	0.89[ASN][1000 genomes]
rs12455909	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12457760	0.84[CEU][hapmap]
rs12604184	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs12604385	0.85[ASN][1000 genomes]
rs12604400	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12604541	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12605240	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12605392	0.81[ASN][1000 genomes]
rs12606506	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12709540	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12953406	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12954614	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12955161	0.99[ASN][1000 genomes]
rs12955490	0.97[ASN][1000 genomes]
rs12956385	0.88[ASN][1000 genomes]
rs12956885	0.80[ASN][1000 genomes]
rs12957151	0.90[ASN][1000 genomes]
rs12957688	0.83[ASN][1000 genomes]
rs12958200	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12959015	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12961695	0.89[ASN][1000 genomes]
rs12961966	0.96[ASN][1000 genomes]
rs12962476	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12963179	0.83[ASN][1000 genomes]
rs12963325	0.84[ASN][1000 genomes]
rs12964660	0.94[ASN][1000 genomes]
rs12965094	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12969567	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs12970025	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12970174	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17615158	0.84[CEU][hapmap];0.84[MKK][hapmap]
rs17616402	0.89[YRI][hapmap]
rs1864532	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1893193	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1940974	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1940975	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2155698	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2186907	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs28414067	0.81[ASN][1000 genomes]
rs28496036	0.85[ASN][1000 genomes]
rs28582228	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28886423	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34072260	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34178879	0.96[ASN][1000 genomes]
rs34438212	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34456643	0.94[ASN][1000 genomes]
rs34814556	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34899007	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35122110	0.85[ASN][1000 genomes]
rs35449211	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35630805	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35963756	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4389196	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4493131	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55749182	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58215411	0.96[ASN][1000 genomes]
rs60505421	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62097094	0.88[ASN][1000 genomes]
rs62097102	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62097103	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62097126	0.85[ASN][1000 genomes]
rs62097148	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62097149	0.80[ASN][1000 genomes]
rs62097153	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67045810	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67268432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722708	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7233175	0.89[YRI][hapmap]
rs7234697	0.83[ASN][1000 genomes]
rs7237732	0.82[CHB][hapmap]
rs723836	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7238546	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7242395	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs755020	0.81[ASN][1000 genomes]
rs755021	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8086094	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs8087885	0.85[ASN][1000 genomes]
rs8088786	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8089081	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8093129	0.80[ASN][1000 genomes]
rs8093532	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs8093571	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8095160	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs9303772	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9303773	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs948301	0.85[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs948302	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9675543	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9945339	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9947738	0.80[ASN][1000 genomes]
rs9949582	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9951147	0.85[ASN][1000 genomes]
rs9954054	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs9958666	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9959759	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9960824	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9961705	0.81[EUR][1000 genomes]
rs9961851	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9964759	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9989506	0.90[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv2756075	chr18:12481377-12548970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12457903	SPIRE1	cis	Liver	GTEx
rs12457903	SPIRE1	cis	Muscle Skeletal	GTEx
rs12457903	CEP76	cis	cerebellum	SCAN
rs12457903	RP11-861E21.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
2	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
3	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr18:12511400-12551800	Weak transcription	Lung	lung
5	chr18:12516000-12553200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:12516600-12555000	Weak transcription	Aorta	Aorta
7	chr18:12518600-12551800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:12520800-12551800	Weak transcription	Colon Smooth Muscle	Colon
9	chr18:12520800-12552000	Weak transcription	NHLF	lung
10	chr18:12521000-12552200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr18:12530600-12551600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:12533200-12551800	Weak transcription	HSMMtube	muscle
13	chr18:12534000-12551800	Weak transcription	Fetal Brain Male	brain
14	chr18:12534600-12551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:12541000-12551800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr18:12541000-12552000	Weak transcription	Gastric	stomach
17	chr18:12541400-12553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr18:12542600-12551800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:12542600-12551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr18:12543200-12550400	Weak transcription	HUVEC	blood vessel
21	chr18:12543400-12551600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr18:12543600-12551800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr18:12543800-12548200	Weak transcription	Fetal Lung	lung
24	chr18:12543800-12551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:12543800-12551800	Weak transcription	NH-A	brain
26	chr18:12543800-12552000	Weak transcription	Fetal Muscle Leg	muscle
27	chr18:12544000-12551800	Weak transcription	HSMM	muscle
28	chr18:12544200-12551600	Weak transcription	HMEC	breast
29	chr18:12544800-12551800	Weak transcription	Liver	Liver
30	chr18:12545200-12553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr18:12545600-12553000	Weak transcription	Psoas Muscle	Psoas
32	chr18:12546800-12550200	Weak transcription	Left Ventricle	heart
33	chr18:12546800-12551800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:12546800-12551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:12546800-12557000	Weak transcription	Ovary	ovary
36	chr18:12547000-12548800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:12547000-12549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:12547000-12551800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr18:12547400-12547600	Enhancers	Brain Germinal Matrix	brain
40	chr18:12547400-12548000	Enhancers	Fetal Brain Female	brain

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