Variant report

Variant	rs4894286
Chromosome Location	chr3:134908179-134908180
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134907680..134909883-chr3:134915738..134918698,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1021753	0.99[ASN][1000 genomes]
rs1021754	0.99[ASN][1000 genomes]
rs1027608	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1501195	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16842755	0.94[JPT][hapmap]
rs1875371	0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28594191	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35779003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772636	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs3772638	0.83[MEX][hapmap]
rs3821502	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4441681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569682	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894257	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894258	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894280	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894287	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4894290	0.92[EUR][1000 genomes]
rs6763009	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6776570	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6799448	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799471	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875368	0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875370	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs882059	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs882060	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822213	0.88[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837009	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4894286	CEP63	cis	parietal	SCAN
rs4894286	KY	cis	cerebellum	SCAN
rs4894286	TXNDC6	cis	cerebellum	SCAN
rs4894286	SLC38A2	trans	parietal	SCAN
rs4894286	PPP2R3A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134885600-134911800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:134887600-134911400	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:134888200-134908600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:134889000-134910200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
7	chr3:134895800-134912000	Weak transcription	Brain Angular Gyrus	brain
8	chr3:134901600-134910000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:134901800-134911400	Weak transcription	Fetal Brain Female	brain
10	chr3:134906600-134909600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:134907000-134910000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:134907200-134913400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:134907400-134922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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