Variant report

Variant	rs6763009
Chromosome Location	chr3:134915188-134915189
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1027608	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1501195	0.88[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs28594191	0.90[ASN][1000 genomes]
rs35779003	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772636	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821502	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4441681	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4569682	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs4894257	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894258	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894280	0.87[EUR][1000 genomes]
rs4894286	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]
rs4894287	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4894289	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894290	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439561	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6766459	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6776570	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6799448	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs6799471	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs875368	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs875369	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs882060	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9822213	0.92[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs9824249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9837009	0.82[AMR][1000 genomes];0.93[EUR][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
rs6763009	CEP63	cis	parietal	SCAN
rs6763009	TXNDC6	cis	cerebellum	SCAN
rs6763009	PPP2R3A	cis	parietal	SCAN
rs6763009	SLC38A2	trans	parietal	SCAN
rs6763009	KY	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
2	chr3:134907400-134922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:134909000-134932400	Weak transcription	Psoas Muscle	Psoas
4	chr3:134910000-134926400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:134910200-134923400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:134910800-134932600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:134911000-134922000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:134912600-134916600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:134912600-134923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:134912800-134916200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:134913600-134920000	Weak transcription	Fetal Brain Female	brain
12	chr3:134913800-134935600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:134914200-134915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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