Variant report

Variant	rs2963774
Chromosome Location	chr5:114629356-114629357
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114623240..114626730-chr5:114627807..114632536,6	MCF-7	breast:
2	chr5:114626278..114629451-chr5:114630853..114633217,3	K562	blood:
3	chr5:114626278..114630090-chr5:114630456..114633226,5	K562	blood:
4	chr5:114590810..114593401-chr5:114627414..114629564,2	MCF-7	breast:
5	chr5:114627696..114629421-chr5:114959972..114962333,2	K562	blood:

Variant related genes	Relation type
ENSG00000243414	Chromatin interaction
ENSG00000251201	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000250197	Chromatin interaction
ENSG00000164221	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10059320	0.82[JPT][hapmap]
rs10077453	0.85[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1017208	0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs11950355	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs13152930	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13172537	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17459144	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2305130	0.91[JPT][hapmap]
rs28379874	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909842	0.89[ASN][1000 genomes]
rs2909843	0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2925185	0.92[ASN][1000 genomes]
rs2963769	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2963770	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2963771	0.95[CEU][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963772	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963773	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2964543	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2964544	0.90[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34434304	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35948019	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4041	0.91[JPT][hapmap]
rs4705732	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7734074	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs9326953	0.80[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9326956	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2963774	PGGT1B	cis	lesional skin	skin_eQTL
rs2963774	PGGT1B	cis	uninvolved skin	skin_eQTL
rs2963774	PGGT1B	cis	multi-tissue	Pritchard
rs2963774	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
2	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:114599000-114631200	Weak transcription	HSMM	muscle
4	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
5	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:114601200-114631200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:114601200-114631400	Weak transcription	Aorta	Aorta
8	chr5:114604000-114630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:114611200-114630400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:114611200-114630400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:114611200-114630800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:114612800-114630200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:114621600-114630400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:114622400-114630200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:114625400-114630600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:114625400-114630800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:114627000-114631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:114627400-114630600	Weak transcription	NHLF	lung
19	chr5:114628000-114631200	Weak transcription	Fetal Kidney	kidney
20	chr5:114628200-114629600	ZNF genes & repeats	Fetal Brain Female	brain
21	chr5:114628600-114629400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr5:114628600-114629600	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr5:114628600-114630000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:114628600-114630400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:114628600-114630800	Weak transcription	Colonic Mucosa	Colon
26	chr5:114628600-114631200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:114628600-114631400	Weak transcription	Esophagus	oesophagus
28	chr5:114628800-114630600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:114629000-114629600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:114629000-114630200	Weak transcription	Fetal Brain Male	brain
31	chr5:114629000-114630800	Weak transcription	Primary B cells from cord blood	blood
32	chr5:114629000-114631200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:114629000-114631200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:114629200-114630200	Weak transcription	Hela-S3	cervix

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