Variant report

Variant	rs1017208
Chromosome Location	chr5:114602129-114602130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114598026..114600265-chr5:114601043..114603821,2	K562	blood:
2	chr5:114598208..114599898-chr5:114601355..114602888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271797	Chromatin interaction
ENSG00000164219	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10059320	0.91[JPT][hapmap]
rs10077453	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11950355	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17459144	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2305130	1.00[JPT][hapmap]
rs28379874	0.96[ASN][1000 genomes]
rs2909842	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2909843	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925185	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2925186	0.81[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2963769	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2963770	0.84[CEU][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963771	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2963772	1.00[ASN][1000 genomes]
rs2963773	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2963774	0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs2964543	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2964544	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35948019	0.96[ASN][1000 genomes]
rs4041	1.00[JPT][hapmap]
rs4705732	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7734074	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326953	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv968977	chr5:114599737-114602288	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1017208	PGGT1B	cis	lesional skin	skin_eQTL
rs1017208	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs1017208	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114598800-114602600	Weak transcription	Spleen	Spleen
2	chr5:114598800-114608200	Weak transcription	Small Intestine	intestine
3	chr5:114598800-114612200	Weak transcription	Gastric	stomach
4	chr5:114598800-114613000	Weak transcription	Esophagus	oesophagus
5	chr5:114599000-114603200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:114599000-114606200	Weak transcription	HSMMtube	muscle
7	chr5:114599000-114606400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:114599000-114606400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:114599000-114608800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:114599000-114610200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:114599000-114610200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:114599000-114610400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:114599000-114610600	Weak transcription	Pancreas	Pancrea
14	chr5:114599000-114610600	Weak transcription	NHLF	lung
15	chr5:114599000-114612200	Weak transcription	Right Ventricle	heart
16	chr5:114599000-114612800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:114599000-114612800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:114599000-114612800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:114599000-114612800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:114599000-114612800	Weak transcription	Fetal Intestine Large	intestine
21	chr5:114599000-114612800	Weak transcription	Fetal Thymus	thymus
22	chr5:114599000-114614200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:114599000-114617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:114599000-114617200	Weak transcription	Thymus	Thymus
25	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
28	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:114599000-114631200	Weak transcription	HSMM	muscle
30	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
31	chr5:114599200-114602400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:114599200-114602400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:114599200-114603000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:114599200-114603000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:114599200-114603000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:114599200-114603000	Weak transcription	NHDF-Ad	bronchial
37	chr5:114599200-114603200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:114599200-114603400	Weak transcription	Osteobl	bone
39	chr5:114599200-114603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:114599200-114603600	Weak transcription	HUVEC	blood vessel
41	chr5:114599200-114606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:114599200-114606200	Weak transcription	Primary T cells from cord blood	blood
43	chr5:114599200-114606200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:114599200-114606200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:114599200-114606400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:114599200-114606400	Weak transcription	Primary B cells from cord blood	blood
47	chr5:114599200-114606400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:114599200-114606400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:114599200-114608000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:114599200-114608000	Weak transcription	Adipose Nuclei	Adipose

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