Variant report

Variant	rs267288
Chromosome Location	chr5:114645682-114645683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114645624..114646196-chr5:114709538..114710375,2	MCF-7	breast:
2	chr5:114645138..114646056-chr5:114908059..114908645,2	MCF-7	breast:
3	chr5:114644466..114646908-chr5:114878278..114881087,2	MCF-7	breast:
4	chr5:114645305..114646120-chr5:115403049..115404011,2	K562	blood:
5	chr5:114645535..114646139-chr5:114921972..114922517,2	MCF-7	breast:
6	chr5:114645258..114646128-chr5:114921954..114922997,3	K562	blood:
7	chr5:114645171..114646099-chr5:114908180..114909218,4	K562	blood:

Variant related genes	Relation type
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs117060	0.85[CEU][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs17137637	0.83[AMR][1000 genomes]
rs185566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112360	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112361	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124396	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2545430	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs267286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs267292	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs267295	0.83[CHB][hapmap];0.94[AMR][1000 genomes]
rs267299	0.85[CEU][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267300	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267301	0.85[CEU][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs267302	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267304	0.83[CHB][hapmap]
rs267306	0.87[AMR][1000 genomes]
rs267307	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes]
rs3100784	0.81[CEU][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	nsv980960	chr5:114640484-114645980	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs267288	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114642200-114651200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:114642200-114651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:114642400-114647400	Weak transcription	Brain Germinal Matrix	brain
4	chr5:114645600-114646200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:114645600-114648000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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