Table 2.

Genes and communities identified in the Pain Questionnaire cohort associated with phenotypic and clinical features

Gene	SNP (Most severe variant consequence—VEP)	SNP minor allele frequency	Gene association with phenotypic or clinical feature (p-value before multiple testing correction)	Community	Community association with phenotypic or clinical feature (p-value before multiple testing correction)	Gene association replicated in disjoint Verbal Interview Cohort
S100PBP	rs41306603 (3 prime UTR variant)	0.052	Males (p = 0.022)	1	Males (p = 0.016)	No
ATP9A	rs2904106 (intron variant)	0.271	Males (p = 0.016)	1	Males (p = 0.016)	Yes
KCNB1	rs237475 (intron variant)	0.472	Males (p = 0.016)	1	Males (p = 0.016)	No
CLOCK	rs6832769 (3 prime UTR variant)	0.362	Fibromyalgia, ICD-10: M79.7 (p = 0.026); Other soft tissue disorders, ICD-10: M79 (p = 0.044)	2	Fibromyalgia, ICD-10: M79.7 (p = 0.026); Other soft tissue disorders, ICD-10: M79 (p = 0.044)	No
SLC15A4	rs2398428 (intergenic variant)	0.269		3		No
TMEM232	rs58264436 (intergenic variant)	0.394		6		No
GPC5	rs16947237 (intron variant)	0.155		7		No
PHACTR2	rs9403525 (intron variant)	0.448	Thyroiditis, ICD10-10: E06 (p = 0.033)	8	Thyroiditis, ICD10-10: E06 (p = 0.033)	No
AKAP1	rs3785477 (intron variant)	0.398		9		No
USP6NL	rs2499908 (intergenic variant)	0.235		12		No
CDON	rs73021223 (intron variant)	0.093	Illness, injury, bereavement, stress in last 2 years 2014 + (p = 0.023)	13		No
INSR	rs59165976 (intron variant)	0.388		14		No
SLC6A11	rs2304725 (synonymous variant)	0.319	Phenylalanine levels in plasma (p = 0.022); Illness, injury, bereavement, stress in last 2 years 2019 + (p = 0.003)	15	Illness, injury, bereavement, stress in last 2 years 2019 + (p = 0.003)	Yes
SULF2	rs56218501/ Affx-16805420 (missense variant)	0.213	Phenylalanine levels in plasma (p = 0.022); Illness, injury, bereavement, stress in last 2 years 2019 + (p = 0.003)	15	Illness, injury, bereavement, stress in last 2 years 2019 + (p = 0.003)	No