Variant report

Variant	rs2964543
Chromosome Location	chr5:114623745-114623746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114623240..114626730-chr5:114627807..114632536,6	MCF-7	breast:
2	chr5:114619634..114629040-chr5:114629951..114633566,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164221	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10059320	0.91[JPT][hapmap]
rs10077453	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1017208	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]
rs11950355	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17459144	0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305130	1.00[JPT][hapmap]
rs28379874	0.89[ASN][1000 genomes]
rs2909842	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2909843	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2925185	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925186	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2963769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2963770	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2963771	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2963772	0.86[ASN][1000 genomes]
rs2963773	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2963774	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2964544	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs35948019	0.89[ASN][1000 genomes]
rs4041	1.00[JPT][hapmap]
rs4705732	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7734074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9326953	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv968978	chr5:114620599-114625007	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2964543	PGGT1B	cis	lymphoblastoid	seeQTL
rs2964543	CCDC112	cis	parietal	SCAN
rs2964543	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs2964543	PGGT1B	cis	multi-tissue	Pritchard
rs2964543	PGGT1B	cis	lesional skin	skin_eQTL

Chromatin state (count:25 , 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	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:114601200-114631200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:114601200-114631400	Weak transcription	Aorta	Aorta
10	chr5:114604000-114630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:114611200-114630400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:114611200-114630400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:114611200-114630800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:114611400-114624200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:114611400-114627600	Weak transcription	Primary B cells from cord blood	blood
16	chr5:114611400-114628600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:114612400-114625000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:114612800-114630200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:114621400-114628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:114621600-114628400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:114621600-114630400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:114622200-114625000	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:114622200-114625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:114622400-114624200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:114622400-114630200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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