Variant report

Variant	rs296429
Chromosome Location	chr6:133727421-133727422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs120490	0.95[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159417	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159418	0.91[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs159423	0.96[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159424	0.90[EUR][1000 genomes]
rs212808	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs296422	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs296426	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs296428	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296430	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025700	chr6:133726264-133748758	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv604699	chr6:133726502-133747840	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1019755	chr6:133726502-133748758	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1020698	chr6:133726502-133751161	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv525971	chr6:133726646-133753825	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs296429	VNN3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133716000-133728600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:133718200-133728600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:133719800-133728200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:133720200-133748400	Weak transcription	Hela-S3	cervix
5	chr6:133720400-133749600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:133723400-133728200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:133723400-133728600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:133725600-133728600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:133726000-133727600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:133726000-133728600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:133726400-133727600	Enhancers	Psoas Muscle	Psoas
12	chr6:133726400-133727600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:133726400-133728400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:133726600-133752200	Weak transcription	Right Atrium	heart

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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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