Variant report

Variant	rs267298
Chromosome Location	chr5:114618222-114618223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114616553..114619360-chr5:114629517..114632086,3	MCF-7	breast:
2	chr5:114607630..114609862-chr5:114615334..114618265,2	MCF-7	breast:
3	chr5:114614199..114617138-chr5:114617359..114621851,4	K562	blood:
4	chr5:114618112..114620464-chr5:114620662..114622678,3	K562	blood:

Variant related genes	Relation type
ENSG00000164221	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10076833	0.81[TSI][hapmap]
rs117060	1.00[CHB][hapmap]
rs11745083	0.82[CEU][hapmap]
rs11745170	0.82[CEU][hapmap]
rs155414	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs155573	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs169088	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17459144	0.83[YRI][hapmap]
rs185566	0.89[CHD][hapmap]
rs2053697	0.89[CEU][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303001	0.82[CEU][hapmap]
rs265412	0.85[CHD][hapmap]
rs265419	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs265420	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs265421	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs265425	0.89[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs265430	0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs265435	0.92[CHB][hapmap]
rs265436	0.83[CHB][hapmap]
rs265439	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs265442	0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs267286	0.89[CHD][hapmap]
rs267295	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs267297	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	1.00[CHB][hapmap]
rs267300	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs267301	1.00[CHB][hapmap]
rs267302	0.91[CHB][hapmap]
rs267303	0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs267304	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267307	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs3100784	1.00[CHB][hapmap];0.93[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs267298	PGGT1B	cis	lesional skin	skin_eQTL
rs267298	CCDC112	cis	parietal	SCAN
rs267298	PGGT1B	cis	normal skin	skin_eQTL
rs267298	PGGT1B	cis	uninvolved skin	skin_eQTL
rs267298	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs267298	PGGT1B	cis	lymphoblastoid	seeQTL
rs267298	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
4	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:114599000-114631200	Weak transcription	HSMM	muscle
6	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
7	chr5:114599200-114622000	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:114599400-114621800	Weak transcription	Brain Angular Gyrus	brain
10	chr5:114601200-114631200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:114601200-114631400	Weak transcription	Aorta	Aorta
12	chr5:114602800-114621800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:114604000-114622400	Weak transcription	NHDF-Ad	bronchial
14	chr5:114604000-114630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:114610000-114621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:114610400-114621400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:114610800-114621800	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:114611200-114618400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:114611200-114618600	Weak transcription	Brain Germinal Matrix	brain
20	chr5:114611200-114619000	Weak transcription	HSMMtube	muscle
21	chr5:114611200-114621800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:114611200-114622000	Weak transcription	Adipose Nuclei	Adipose
23	chr5:114611200-114622000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:114611200-114630400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:114611200-114630400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:114611200-114630800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:114611400-114618800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:114611400-114621200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:114611400-114624200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:114611400-114627600	Weak transcription	Primary B cells from cord blood	blood
31	chr5:114611400-114628600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:114611600-114619800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:114611600-114622200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr5:114611600-114623200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:114612400-114621600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:114612400-114625000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:114612600-114619000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:114612800-114621200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:114612800-114622400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:114612800-114630200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:114615800-114621400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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