- Has SubmitterLinkOut (From SNP->SubSNP->Batch.link_out)
- SNP is Precious (Clinical,Pubmed Cited)
- Provisional Third Party Annotation(TPA)(currently rs from PHARMGKB who will give pheotype data).
- Links exist to PubMed Central article
- In Intron (FxnCode = 6)
- Has reference (A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8)
- Has synonymous (A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3)
- Is Assembly specific. (This bit is 1 if the snp only maps to one assembly.)
- Weight=1. (Weight on NCBI reference assembly.)
- Is Validated. (The snp has 2+ minor allele count based on frequency or genotype data.)
- >5% minor allele frequency in each and all populations.
- >5% minor allele frequency in 1+ populations
- Marker is on high density genotyping kit (50K density or greater). The snp may have phenotype associations present in dbGaP.
- Genotypes available. The snp has individual genotype (in SubInd table).
- 1000 Genome Phase 1 ( include June Interim phase 1)
- RS Cluster has TGP Submission as of June 2011 (include all current RS from TGP): VCF - KGPROD
- RS Cluster has none TGP Submission(set VCF OTHERKG).
- HapMap Phase 3 genotyped: filtered, non- redundant. (VCF: PH3)
- Single base polymorphism SNP
- Has Genotype Conflict Same (rs, ind), different genotype. N/N is not included.