Variant report

Variant	rs12457026
Chromosome Location	chr18:12551818-12551819
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	chr18:12541118..12543753-chr18:12550923..12553850,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1062235	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs11080581	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1129214	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11874852	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs12373207	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12457771	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap]
rs12458000	1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12960623	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12966424	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs12967204	1.00[YRI][hapmap]
rs12968771	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12969446	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs12971041	0.89[MKK][hapmap];1.00[YRI][hapmap]
rs1362709	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs1549011	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1592643	0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs17616402	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs2302768	0.94[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs3902981	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs4296322	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs4633785	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs55634668	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57010148	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6505760	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs7229168	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7233175	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9303774	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9303775	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs948319	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs9945801	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs9952000	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs9955985	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs9958100	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs9961799	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs9962006	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs9963809	0.89[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12457026	PSMG2	cis	cerebellum	SCAN
rs12457026	CEP76	cis	cerebellum	SCAN
rs12457026	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs12457026	SPIRE1	cis	Muscle Skeletal	GTEx
rs12457026	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL
rs12457026	PSMG2	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12516000-12553200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:12516600-12555000	Weak transcription	Aorta	Aorta
3	chr18:12520800-12552000	Weak transcription	NHLF	lung
4	chr18:12521000-12552200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr18:12541000-12552000	Weak transcription	Gastric	stomach
6	chr18:12541400-12553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12543800-12552000	Weak transcription	Fetal Muscle Leg	muscle
8	chr18:12545200-12553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr18:12545600-12553000	Weak transcription	Psoas Muscle	Psoas
10	chr18:12546800-12557000	Weak transcription	Ovary	ovary
11	chr18:12550200-12552600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:12551600-12552600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr18:12551600-12553800	Enhancers	HMEC	breast
14	chr18:12551800-12552000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr18:12551800-12552000	Enhancers	Brain Anterior Caudate	brain
16	chr18:12551800-12552000	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr18:12551800-12552200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:12551800-12552200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:12551800-12552200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr18:12551800-12552200	Enhancers	Fetal Brain Male	brain
21	chr18:12551800-12552200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr18:12551800-12552400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr18:12551800-12552400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:12551800-12552400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:12551800-12552400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr18:12551800-12552400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr18:12551800-12552400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr18:12551800-12552400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:12551800-12552400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr18:12551800-12552400	Flanking Active TSS	Liver	Liver
31	chr18:12551800-12552400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr18:12551800-12552400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr18:12551800-12552400	Enhancers	Colon Smooth Muscle	Colon
34	chr18:12551800-12552400	Enhancers	Right Atrium	heart
35	chr18:12551800-12552400	Enhancers	HSMM	muscle
36	chr18:12551800-12552400	Enhancers	HSMMtube	muscle
37	chr18:12551800-12552400	Enhancers	NH-A	brain
38	chr18:12551800-12552400	Flanking Active TSS	Osteobl	bone
39	chr18:12551800-12552600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr18:12551800-12552600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:12551800-12552600	Enhancers	Brain Substantia Nigra	brain
42	chr18:12551800-12552600	Enhancers	Fetal Brain Female	brain
43	chr18:12551800-12552600	Enhancers	Pancreas	Pancrea
44	chr18:12551800-12552600	Enhancers	Stomach Smooth Muscle	stomach
45	chr18:12551800-12553000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr18:12551800-12553200	Enhancers	Brain Angular Gyrus	brain
47	chr18:12551800-12553400	Enhancers	Stomach Mucosa	stomach
48	chr18:12551800-12553600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr18:12551800-12553600	Enhancers	Adipose Nuclei	Adipose
50	chr18:12551800-12553600	Enhancers	Right Ventricle	heart

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