Table 3.

Genes with $\ge 20$ significant CpG sites.

Gene name	Chr	# of significant CpG Sites	Function and conditions related to changes in gene
PTPRN2	7	87	Encodes a protein that is an autoantigen in type 1 diabetes (Olsson et al. 2014); regulation of insulin secretion; involvement with insulin-dependent diabetes mellitus as an autoantigen (Li et al. 1997).
MAD1L1	7	46	Component of mitotic spindle-assembly checkpoint that prevents onset of anaphase until all chromosomes are properly aligned at metaphase plate (Ji et al. 2018; Jin et al. 1999; Nakano et al. 2010); this may play role in cell cycle control and tumor suppression (Li et al. 2016).
PRDM16	1	35	Chromosomal aberration involving this gene is found in myelodysplastic syndrome and acute myeloid leukemia (Xinh et al. 2003); functions in the differentiation of brown adipose tissue (Moreno-Navarrete et al. 2018); suppressor of lung adenocarcinoma metastasis (Fei et al. 2019).
ATP11A	13	34	Predictive marker for metachronous metastasis of colorectal cancer (Miyoshi et al. 2010); associated with bronchiectasis (persistent abnormal dilation of the bronchi) and clubbed fingers.
DIP2C	10	33	Loss of DIP2C homolog in rat knock-outs stimulates changes in DNA methylation and epithelial-mesenchymal transition (Larsson et al. 2017); expression in breast cancer (Li et al. 2017).
CAMTA1	1	29	Associated with cerebellar ataxia with mental retardation (neurodevelopmental disorder characterized by mildly delayed psychomotor development, early onset of cerebellar ataxia, and intellectual disability in childhood and adulthood) (Thevenon et al. 2012); immunohistochemical marker for diagnosing epithelioid hemangioendothelioma (Shibuya et al. 2015).
ARHGEF10	8	28	Mutations in this gene are associated with slowed nerve conduction velocity, without any clinical signs of peripheral or central nervous system dysfunction (Verhoeven et al. 2003), and Charcot-Marie-Tooth disease (Boora et al. 2015).
INPP5A	10	28	Mobilizes intracellular calcium and acts as a second messenger mediating cell response to various stimulation; ataxia and cerebellar degeneration in mice (Yang et al. 2015).
TBCD	17	28	Required for correct assembly and maintenance of the mitotic spindle, and proper progression of mitosis; genetic changes can result in early-onset, progressive encephalopathy, and with brain atrophy and thin corpus callosum (an autosomal recessive disease with neurodevelopmental and neurodegenerative features) (Flex et al. 2016).
HDAC4	2	25	Provides instructions for making histone deacetylase 4; involved in the regulation of activity of genes involved in heart and skeletal development and nerve cell survival; mutation in the HDAC4 gene is associated with brachydactyly with no other health problems, intellectual disability, behavioral problems, and skeletal abnormalities (Williams et al. 2010).
RASA3	13	25	Inhibitory regulator of the Ras-cyclic AMP pathway (Molina-Ortiz et al. 2018); functions as a negative regulator of the Ras signaling pathway (Schurmans et al. 2015).
AGAP1	2	24	Functions as a direct regulator of the adaptor-related protein complex 3 on endosomes (Nie et al. 2005); rare variants in this gene have been identified with autism (Pacault et al. 2019).
RPTOR	17	24	Encodes a protein that functions in cell-signaling pathway that responds to nutrient and insulin levels to regulate cell growth (Kim et al. 2002); has a positive role in maintaining cell size and mTOR protein expression, which plays a role in mRNA translation, autophagy, and cell growth; dysregulation of the mTOR pathway has been associated with cancer (Xie and Sun 2019).
SHANK2	11	21	May play a role in the structural and functional organization of the dendritic spine and synaptic function (MacGillavry et al. 2016) and regulate the molecular structure of Shank and the spectrum of Shank-interacting proteins in the postsynaptic densities of the adult and developing brain; mutations in this gene have been associated with autism spectrum disorder (Leblond et al. 2014).
TNXB	6	21	Provides instructions for making tenascin-X, which plays an important role in organizing and maintaining the structure of tissues that support the body’s muscles, joints, organs, and skin/connective tissues (Mao et al. 2002); helps to regulate the production and assembly of collagen and elastic fibers in connective tissues (Kolli et al. 2019); mutations in the TNXB gene cause a very small percentage of all cases of a form of Ehlers-Danlos syndrome called the hypermobile type, which is characterized by unusually large range of joint movement (Lao et al. 2020; Micale et al. 2019); a functional variant in the TNXB promoter is associated with the risk of esophageal squamous-cell carcinoma (Yang et al. 2020).
FOXP1	3	20	Has an important role in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood (Liu et al. 2019); may act as a tumor suppressor (Takayama et al. 2014); has been found to promote cancer stem cell-like characteristics in ovarian cancer cells (Choi et al. 2016); mutations resulting in deregulation of its expression plays an important role in the development of lung adenocarcinoma (Sheng et al. 2019) and lymphoma (Goatly et al. 2008); mutations in this gene have resulted in severe intellectual disability syndrome (Meerschaut et al. 2017; Vuillaume et al. 2018) and may play a role in speech and language disorders (Horn et al. 2010; Le Fevre et al. 2013).
SDK1	7	20	Codes for adhesion molecule that promotes lamina-specific synaptic connections in the retina and is expressed in specific subsets of interneurons and retinal ganglion cells (Yamagata et al. 2002); dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy (Kaufman et al. 2004), glomerulosclerosis (Kaufman et al. 2010), and malignant mesothelioma (Cadby et al. 2013).

Note: Chr, chromosome.