Variant report

Variant	rs9403480
Chromosome Location	chr6:143605472-143605473
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1345991	0.82[AMR][1000 genomes]
rs1364650	0.83[AMR][1000 genomes]
rs1559598	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1863137	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1885649	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194655	0.83[AMR][1000 genomes]
rs2216917	0.83[AMR][1000 genomes]
rs2328474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895609	0.83[AMR][1000 genomes]
rs4896644	0.88[AMR][1000 genomes]
rs4896645	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6570555	0.83[AMR][1000 genomes]
rs6901152	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6907215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917403	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6930404	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931802	1.00[CHB][hapmap]
rs6933721	0.86[ASW][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap]
rs7454731	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7738887	0.83[AMR][1000 genomes]
rs7749040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760341	0.83[AMR][1000 genomes]
rs7763696	0.85[AFR][1000 genomes]
rs7766829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373387	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373390	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9376739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376743	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9376745	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9399433	0.85[AFR][1000 genomes]
rs9496542	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs972152	0.83[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9403480	PLAGL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143570800-143609200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:143583400-143606000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:143583800-143615400	Weak transcription	K562	blood
4	chr6:143589000-143607400	Weak transcription	Aorta	Aorta
5	chr6:143592200-143605600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:143593200-143606800	Weak transcription	NHEK	skin
7	chr6:143593400-143607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:143598600-143620200	Weak transcription	Brain Angular Gyrus	brain
9	chr6:143600600-143609200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:143603000-143611000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:143603200-143605600	Weak transcription	HMEC	breast
12	chr6:143603200-143606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:143603200-143607000	Weak transcription	Fetal Heart	heart
14	chr6:143603200-143609600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:143603200-143616800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:143603200-143622200	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:143604000-143605800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:143604400-143605800	Enhancers	Ovary	ovary
19	chr6:143604600-143607800	Weak transcription	Lung	lung
20	chr6:143604800-143608000	Weak transcription	Esophagus	oesophagus
21	chr6:143604800-143608200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:143604800-143609200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:143605000-143606400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:143605000-143608400	Enhancers	Osteobl	bone
25	chr6:143605200-143605800	Enhancers	NH-A	brain
26	chr6:143605200-143606600	Enhancers	Colon Smooth Muscle	Colon
27	chr6:143605200-143608600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:143605200-143608800	Enhancers	Fetal Stomach	stomach
29	chr6:143605200-143610400	Strong transcription	Liver	Liver
30	chr6:143605400-143605600	Strong transcription	HepG2	liver
31	chr6:143605400-143605800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:143605400-143605800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:143605400-143606400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:143605400-143606800	Enhancers	Fetal Muscle Leg	muscle
35	chr6:143605400-143607600	Enhancers	Stomach Smooth Muscle	stomach
36	chr6:143605400-143614600	Weak transcription	NHDF-Ad	bronchial

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