Variant report

Variant	rs12199427
Chromosome Location	chr6:38479060-38479061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10484856	0.87[CEU][hapmap];1.00[AFR][1000 genomes]
rs1073900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947750	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12154188	0.83[CEU][hapmap];1.00[AFR][1000 genomes]
rs12193868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12198294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12206218	0.87[CEU][hapmap];1.00[AFR][1000 genomes]
rs12206371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12208087	0.87[CEU][hapmap];1.00[AFR][1000 genomes]
rs1406841	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes]
rs1699015	0.85[GIH][hapmap];0.84[TSI][hapmap]
rs1699018	0.85[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs17543429	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs2748156	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs2748173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs2814887	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2814890	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs28616055	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4074421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254983	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55869483	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56083119	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56250767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903004	0.87[CEU][hapmap]
rs6924443	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs6927145	0.81[CEU][hapmap]
rs72853429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743871	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752239	0.83[CEU][hapmap]
rs7755619	0.82[CEU][hapmap]
rs7761154	0.80[EUR][1000 genomes]
rs7767041	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12199427	GLO1	cis	cerebellum	SCAN
rs12199427	ANKS1A	cis	cerebellum	SCAN
rs12199427	GLO1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38468600-38486400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:38471600-38484200	Weak transcription	Right Atrium	heart
6	chr6:38471600-38493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:38472000-38482400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:38472000-38493800	Weak transcription	Lung	lung
9	chr6:38472400-38481800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:38476600-38499800	Weak transcription	Pancreas	Pancrea
11	chr6:38476800-38481400	Weak transcription	Fetal Brain Male	brain
12	chr6:38476800-38481800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:38476800-38498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:38477000-38481600	Weak transcription	Brain Anterior Caudate	brain
15	chr6:38477400-38482400	Weak transcription	Fetal Stomach	stomach
16	chr6:38477800-38498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:38478000-38480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:38478000-38481200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:38478000-38482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:38478000-38484800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:38478000-38484800	Weak transcription	Fetal Lung	lung
22	chr6:38478000-38485000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:38478000-38485000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:38478000-38485200	Weak transcription	Gastric	stomach
25	chr6:38478000-38494800	Weak transcription	Fetal Kidney	kidney
26	chr6:38478200-38480200	Weak transcription	NHLF	lung
27	chr6:38478200-38481800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:38478200-38482200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:38478200-38484200	Weak transcription	Ovary	ovary
30	chr6:38478200-38484800	Weak transcription	NHDF-Ad	bronchial
31	chr6:38478400-38486200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:38478800-38480000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:38478800-38480000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:38479000-38509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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