APOE

ApoE status is defined by these two SNPs:

• rs429358
• rs7412

rs429358 is located in the fourth exon of the ApoE gene (19:45411941)^{(note this position is for reference genome GRCh37.p13)}, affects the amino acid at position 130 of the resulting protein; the more common allele is rs429358(T)(ref). If this allele is rs429358(C)(alt) and the same chromosome also harbors rs7412(C)(ref) allele, the combination is known as an APOE-ε4 allele.

   SNP        CHR   POS(GRCh37)   POS(GRCh38)  REF   ALT   MUT
   rs429358   19    45411941      44908684     T     C     missense
   rs7412     19    45412079      44908822     C     T     missense

Various combinations of SNPs that constitute APOE alleles: ε2 ε3 ε4

   APOE ε2   |  rs429358( T ) + rs7412( T )
   
   APOE ε3   |  rs429358( T ) + rs7412( C )
   
   APOE ε4   |  rs429358( C ) + rs7412( C )

Combinations of BI-CHROMOSOMAL SNPs that constitute APOE alleles: ε2 ε3 ε4

   APOE STATUS (GRCh37 CHR19:POSITION) 		
   APOE 2	45411941 ( T )	45412079 ( T )
   APOE 3	45411941 ( T )	45412079 ( C )
   APOE 4	45411941 ( C )	45412079 ( C )

   APOE 2/2	45411941 ( T , T )	45412079 ( T , T )
   APOE 2/3	45411941 ( T , T )	45412079 ( T , C )
   APOE 2/4	45411941 ( T , C )	45412079 ( T , C )
   APOE 3/3	45411941 ( T , T )	45412079 ( C , C )
   APOE 3/4	45411941 ( T , C )	45412079 ( C , C )
   APOE 4/4	45411941 ( C , C )	45412079 ( C , C )

APOE ε2 ε3 ε4 Allele Chromosomal Combinations

APOE STATUS	GRCh37 CHR19
ALLELE	POS	SNP1	SNP2	POS	SNP1	SNP2
APOE 2/2	45411941	T	T	45412079	T	T
APOE 2/3	45411941	T	T	45412079	T	C
APOE 2/4	45411941	T	C	45412079	T	C
APOE 3/3	45411941	T	T	45412079	C	C
APOE 3/4	45411941	T	C	45412079	C	C
APOE 4/4	45411941	C	C	45412079	C	C

GENOMIC LOCATIONS

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	SNP	CHR	GRCh37.p13	GRCh38.p7	REF	ALT
	rs429358	19	45411941	44908684	T	C
	rs7412	19	45412079	44908822	C	T

MORE DETAILS

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One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Note: Although ApoE status is technically defined by these two SNPs, rs429358 and rs7412, a SNP in the adjacent ApoC1 gene, rs4420638, is co-inherited with ApoE and thus often - though not completely - predictive of it.

SNP VIEWER

   SNP NAME 
   GCTGGGCGCGGACATGGAGGACGTG[C/T]GCGGCCGCCTGGTGCAGTACCGCGG
   NC_000019.9  @ 45411941 @GRCh37.p13 : 19:45411941
   NC_000019.10 @ 44908684 @GRCh38.p7  : 19:45411941
   Variation ID:	rs429358
   Variant Type:	SNP, length 1
   Alleles:	    C/T

SNP VIEWER

   SNP NAME
   NC_000019.9  @ 45412079 @GRCh37.p13 : 19:45412079
   NC_000019.10 @ 44908822 @GRCh38.p7  : 19:44908822
   Variation ID:	rs7412
   Variant Type:	SNP, length 1
   Alleles:	    C/T

APOE on GNOMAD

Get more info about APOE variants on the GNOMAD database provided by a great team of genomics scientists at Broad institute. For convenience, I've pulled the relevant AD-related APOE loci (along with several nearby flanking positions) from GNOMAD and pasted them into this csv datatable.

Usage

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