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

Once installed, you can use "syntaxhighlight" tags on wiki pages. For example,

def quickSort(arr):
	less = []
	pivotList = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass

is the result of the following wikitext markup:

<syntaxhighlight lang="python" line='line'>
def quickSort(arr):
	less = []
	pivotList = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass
</syntaxhighlight>