Variant report

Variant	rs882059
Chromosome Location	chr3:134903412-134903413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1021753	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021754	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027608	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1501195	0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16842755	0.94[JPT][hapmap]
rs1875371	0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35779003	0.95[ASN][1000 genomes]
rs4441681	0.99[ASN][1000 genomes]
rs4569682	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4894253	0.88[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4894257	0.99[ASN][1000 genomes]
rs4894258	0.99[ASN][1000 genomes]
rs4894280	0.96[ASN][1000 genomes]
rs4894286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4894287	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6439561	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs6766459	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs6799448	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6799471	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs875368	0.87[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs875369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs875370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882060	0.99[ASN][1000 genomes]
rs9822213	0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9824249	0.84[CEU][hapmap];0.94[GIH][hapmap];0.83[EUR][1000 genomes]
rs9837009	0.99[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	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs882059	TXNDC6	cis	cerebellum	SCAN
rs882059	PPP2R3A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134885000-134904400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:134885600-134911800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:134887600-134911400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:134888200-134908600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:134889000-134910200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:134890800-134906800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:134895800-134912000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:134901600-134910000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:134901800-134911400	Weak transcription	Fetal Brain Female	brain

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