Variant report

Variant	rs1534024
Chromosome Location	chr3:179684793-179684794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179680245..179682012-chr3:179682933..179685670,2	MCF-7	breast:
2	chr3:179681746..179684175-chr3:179684395..179687260,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10804880	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937014	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464783	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037635	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2140654	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2177589	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4416381	0.81[EUR][1000 genomes]
rs4855126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855127	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770184	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775539	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782786	1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794331	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811817	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824233	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825224	0.84[EUR][1000 genomes]
rs9855801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866978	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867274	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1534024	PEX5L	cis	cerebellum	SCAN
rs1534024	FXR1	cis	parietal	SCAN
rs1534024	FAM131A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179675800-179688000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:179677200-179685000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:179679800-179688000	Weak transcription	Fetal Thymus	thymus
4	chr3:179682200-179686400	Enhancers	Brain Hippocampus Middle	brain
5	chr3:179682200-179688000	Weak transcription	Thymus	Thymus
6	chr3:179682400-179686800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:179682800-179686800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:179683200-179686400	Genic enhancers	Dnd41	blood
9	chr3:179684000-179684800	Enhancers	GM12878-XiMat	blood
10	chr3:179684000-179685400	Enhancers	Brain Anterior Caudate	brain
11	chr3:179684000-179685600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:179684400-179686800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:179684600-179686800	Enhancers	Brain Angular Gyrus	brain

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