Variant report

Variant	rs10059320
Chromosome Location	chr5:114531072-114531073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114528643..114531449-chr5:114541166..114543172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248175	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10055468	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057172	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061960	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070542	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077453	0.91[JPT][hapmap];0.96[MKK][hapmap]
rs10078804	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017208	0.91[JPT][hapmap]
rs11950355	0.91[JPT][hapmap]
rs17459144	0.91[JPT][hapmap]
rs2305130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267304	0.81[MKK][hapmap]
rs2909843	0.91[JPT][hapmap]
rs2963769	0.91[JPT][hapmap]
rs2963770	0.82[JPT][hapmap]
rs2963771	0.91[JPT][hapmap]
rs2963773	0.90[JPT][hapmap]
rs2963774	0.82[JPT][hapmap]
rs2964543	0.91[JPT][hapmap]
rs2964544	0.91[JPT][hapmap]
rs4041	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596375	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705732	0.91[JPT][hapmap]
rs7734074	0.91[JPT][hapmap]
rs9326953	0.91[JPT][hapmap];0.96[MKK][hapmap];0.84[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	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10059320	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs10059320	PGGT1B	cis	multi-tissue	Pritchard
rs10059320	PGGT1B	cis	uninvolved skin	skin_eQTL
rs10059320	PGGT1B	cis	lymphoblastoid	seeQTL
rs10059320	CCDC112	cis	parietal	SCAN
rs10059320	PGGT1B	cis	lesional skin	skin_eQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114522800-114543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
3	chr5:114525400-114531400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr5:114525800-114544800	Weak transcription	Primary T cells from cord blood	blood
5	chr5:114528000-114563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:114529200-114562600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:114529400-114531400	Enhancers	Stomach Mucosa	stomach
8	chr5:114529400-114532000	Enhancers	Duodenum Mucosa	Duodenum
9	chr5:114529600-114531400	Enhancers	Liver	Liver
10	chr5:114529800-114551000	Weak transcription	Left Ventricle	heart
11	chr5:114530000-114531200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:114530200-114562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:114530200-114562600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:114530600-114531200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr5:114530600-114548600	Weak transcription	Fetal Intestine Large	intestine
16	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
17	chr5:114530800-114548000	Weak transcription	Adipose Nuclei	Adipose
18	chr5:114530800-114565200	Weak transcription	NHDF-Ad	bronchial
19	chr5:114531000-114546400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:114531000-114547600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:114531000-114551200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:114531000-114558800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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