Variant report

Variant	rs6439561
Chromosome Location	chr3:134918839-134918840
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1021753	0.84[EUR][1000 genomes]
rs1021754	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1875371	0.84[CEU][hapmap];0.91[GIH][hapmap];0.80[EUR][1000 genomes]
rs28594191	0.89[ASN][1000 genomes]
rs3772636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3821502	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4894289	0.96[ASN][1000 genomes]
rs4894290	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6763009	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6766459	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776570	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs875370	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs882059	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs9824249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6439561	PPP2R3A	cis	parietal	SCAN
rs6439561	TXNDC6	cis	cerebellum	SCAN

Chromatin state (count:11 , 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	chr3:134912600-134923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:134913600-134920000	Weak transcription	Fetal Brain Female	brain
10	chr3:134913800-134935600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:134915200-134922400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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