Variant report

Variant	rs267297
Chromosome Location	chr5:114614047-114614048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs117060	0.84[CHB][hapmap]
rs11745083	0.82[CEU][hapmap]
rs11745170	0.82[CEU][hapmap]
rs155414	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs155573	0.92[ASN][1000 genomes]
rs169088	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs185566	0.86[CHD][hapmap]
rs2053697	0.89[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2303001	0.82[CEU][hapmap]
rs265412	0.82[CHD][hapmap]
rs265418	0.82[ASN][1000 genomes]
rs265419	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs265420	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs265421	0.89[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs265424	0.82[ASN][1000 genomes]
rs265425	0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs265430	0.93[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs265439	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs265442	0.93[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs267286	0.86[CHD][hapmap]
rs267295	0.89[CHD][hapmap]
rs267298	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs267299	0.84[CHB][hapmap]
rs267300	0.89[CHD][hapmap]
rs267301	0.84[CHB][hapmap]
rs267303	0.93[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs267304	0.93[CHD][hapmap]
rs267307	0.89[CHD][hapmap]
rs3100784	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs3805580	0.85[CEU][hapmap]
rs6594883	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6878733	0.82[CEU][hapmap]
rs6886102	0.82[CEU][hapmap]
rs7706217	0.81[CEU][hapmap]
rs7725831	0.82[CEU][hapmap]
rs9326954	0.82[CEU][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs267297	PGGT1B	cis	lesional skin	skin_eQTL
rs267297	CCDC112	cis	parietal	SCAN
rs267297	PGGT1B	cis	multi-tissue	Pritchard
rs267297	PGGT1B	cis	normal skin	skin_eQTL
rs267297	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs267297	PGGT1B	cis	uninvolved skin	skin_eQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114599000-114614200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:114599000-114617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:114599000-114617200	Weak transcription	Thymus	Thymus
4	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
7	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:114599000-114631200	Weak transcription	HSMM	muscle
9	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
10	chr5:114599200-114615000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:114599200-114615000	Weak transcription	Fetal Brain Male	brain
12	chr5:114599200-114616400	Weak transcription	Fetal Heart	heart
13	chr5:114599200-114622000	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:114599400-114615600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:114599400-114621800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:114601200-114631200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:114601200-114631400	Weak transcription	Aorta	Aorta
19	chr5:114602800-114621800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:114604000-114622400	Weak transcription	NHDF-Ad	bronchial
21	chr5:114604000-114630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:114609800-114617600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:114610000-114621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:114610400-114621400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:114610600-114615000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:114610800-114621800	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:114611000-114617800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:114611200-114614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:114611200-114615200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:114611200-114617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:114611200-114618400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:114611200-114618600	Weak transcription	Brain Germinal Matrix	brain
33	chr5:114611200-114619000	Weak transcription	HSMMtube	muscle
34	chr5:114611200-114621800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:114611200-114622000	Weak transcription	Adipose Nuclei	Adipose
36	chr5:114611200-114622000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:114611200-114630400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:114611200-114630400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:114611200-114630800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:114611400-114618800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:114611400-114621200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:114611400-114624200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr5:114611400-114627600	Weak transcription	Primary B cells from cord blood	blood
44	chr5:114611400-114628600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:114611600-114619800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:114611600-114622200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:114611600-114623200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:114612400-114621600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:114612400-114625000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:114612600-114619000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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