Table 2. Genes and selected SNPs in linkage peak, TNFα.

Chromosome	Gene (coverage)a	Short descriptionb	SNP	Position	QTDT addc	QTDT domd
1	CSF1 (58%)	Granulocyte/macrophage colony-stimulating factors are cytokines that act in hematopoiesis by controling the production, differentiation, and function of two related white cell populations of the blood, the granulocytes and the monocytes-macrophages.	rs915357	Intron
			rs333968	Intron	0.055+	0.060+
			rs333970	Intron
			rs3738760	Coding exon
	CD53 (52%)	Cell surface glycoprotein that is known to complex with integrins. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses. Alternative splicing results in multiple transcript variants encoding the same protein.	rs10494122	Intron
			rs10857833	Intron
			rs6679497	Intron	0.012*	0.009**
			rs4839581	Intron
			rs3790722	Intron
	FAM19A3 (100%)	Contains conserved cysteine residues at fixed positions, and are distantly related to MIP-1α, a member of the CC-chemokine family.	rs4450019	Intron	0.019*	0.033*
			rs11102524	Intron
11	MADD (68%)	Tumor necrosis factor alpha (TNFα) is a signaling molecule that interacts with one of two receptors on cells targeted for apoptosis. The protein encoded by this gene is a death domain-containing adaptor protein that interacts with the death domain of TNFα receptor 1 to activate mitogen-activated protein kinase (MAPK) and propagate the apoptotic signal.	rs7114704	Intron
			rs10501320	Intron
			rs10501321	Intron
			rs10838689	Intron
			rs2290149	Intron
			rs11039183	Intron
			rs753993	Intron
	SELH (100%)	This gene encodes a selenoprotein, which contains a selenocysteine (Sec) residue at its active site.	rs9420	Intron boundary
			rs3017889	Downstream
	CD6 (30%)	CD6 is a monomeric 105- or 130-kD membrane glycoprotein that is involved in T-cell activation.	rs2905504	Intron
			rs11230550	Intron
			rs11230553	Intron
			rs2283263	Intron
			rs11230559	Intron
			rs11230563	Coding exon*
			rs2074225	Coding exon*
			rs1050922	Coding exon
	CD5 (68%)	Human T-cell surface glycoprotein of relative molecular mass (Mr) 67 000, has been implicated in the proliferative response of activated T cells and in T-cell helper function.	rs3862667	Intron
			rs572350	Intron
			rs671444	Intron
			rs12364244	Intron
			rs637186	Coding exon*
17	GPS2 (100%)	This gene encodes a protein involved in G protein-mitogen-activated protein kinase (MAPK) signaling cascades.	rs2270981	Coding exon
			rs2292064	Coding exon
	TNFA-SF (80%)	This gene encodes a member of the tumor necrosis factor superfamily. It encodes a hybrid protein composed of the cytoplasmic and transmembrane domains of family member 12 fused to the C-terminal domain of family member 13. The hybrid protein is membrane anchored and presents the receptor-binding domain of family member 13 at the cell surface. It stimulates cycling in T- and B-lymphoma cell lines.	rs9899183	Intron
			rs12937543	Promoter
			rs4968211	Promoter
			rs11552708	Coding Exon*
			rs3803800	Coding Exon*
			rs6608	3'UTR
	CD68 (50%)	This gene encodes a 110-kD transmembrane glycoprotein that is highly expressed by human monocytes and tissue macrophagesThe protein is also a member of the scavenger receptor family. Scavenger receptors typically function to clear cellular debris, promote phagocytosis, and mediate the recruitment and activation of macrophages. Alternative splicing results in multiple transcripts encoding different isoforms.	rs9896688	Intron boundary
			rs9901673	Coding exon*
			rs9901675	Coding exon*

⁺P<0.1; ^*P<0.05; ^**P<0.01.

^aGene coverage was based on genetic variation present in the HapMap database build 18.

^bShort description adapted from gene ontology description provided in the UCSC genome graph tool.

^cP-values reported by QTDT using command WEGA (additive model), tests for association given linkage on a specific locus.

^dP-values reported by QTDT using command WEGD (dominant model), tests for association given linkage on a specific locus.