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Table 3 Top SNPs under “XCI-robust” approach

From: Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder

      XCI-informedXCI-robust
PhenotypeSNPAlleles (min/maj)Nearest geneCohortMAFChosen XCI statusORMORW1ORW2PORMORW1ORW2P
Case statusrs5932307A/GACTRT1Mayo0.08S1.59 (1.04–2.43)1.26 (1.02–1.56)1.59 (1.04–2.43)0.031.39 (0.82–2.36)1.42 (1.00–2.02)2.02 (1.00–4.08)0.06
GAIN0.07S1.60 (1.12–2.30)1.27 (1.06–1.52)1.60 (1.12–2.30)0.011.01 (0.67–1.50)3.54 (2.20–5.69)12.52 (4.85–32.34)6.5E−08
Meta S1.60 (1.21–2.10)1.26 (1.10–1.45)1.60 (1.21–2.10)8.2E−041.13 (0.82–1.56)1.96 (1.48−2.60)3.86 (2.19–6.78)8.3E−08
Rapid cyclingrs5933727G/CTBL1XMayo0.07E*1.91 (1.19–3.06)1.91 (1.19–3.06)3.65 (1.42–9.38)0.011.31 (0.56–3.07)2.25 (1.26–4.02)5.08 (1.60–16.18)0.01
GAIN0.08E*0.38 (0.23–0.62)0.38 (0.23–0.62)0.15 (0.05–0.39)1.2E−040.76 (0.34–1.71)0.27 (0.14–0.51)0.07 (0.02–0.26)3.1E−05
Meta E*0.77 (0.55–1.08)0.77 (0.55–1.08)0.60 (0.30–1.18)0.140.99 (0.55–1.77)0.86 (0.56–1.31)0.73 (0.31–1.73)6.2E−06
Suicide attemptrs5975146A/GXPNPEP2Mayo0.12S0.47 (0.25–0.85)0.68 (0.50–0.92)0.47 (0.25–0.85)0.010.10 (0.02–0.45)0.99 (0.67–1.46)0.98 (0.44–2.15)6.2E−04
GAIN0.11S1.77 (1.09–2.87)1.33 (1.04–1.69)1.77 (1.09–2.87)0.021.07 (0.58–1.99)2.15 (1.39–3.32)4.63 (1.94–11.05)1.7E−03
Meta S1.05 (0.72–1.53)1.02 (0.85–1.24)1.05 (0.72–1.53)0.800.76 (0.43–1.33)1.40 (1.05–1.88)1.97 (1.10–3.53)1.5E−05
Binge eatingrs6627188A/CCNGA2Mayo0.14S0.17 (0.08–0.39)0.41 (0.28–0.62)0.17 (0.08–0.39)2.0E−050.06 (0.01–0.50)0.48 (0.30–0.78)0.23 (0.09–0.61)4.0E−06
GAIN0.13S1.65 (0.86–3.14)1.28 (0.93–1.77)1.65 (0.86–3.14)0.132.00 (0.76–5.27)1.21 (0.78–1.86)1.45 (0.61–3.46)0.31
Meta S0.68 (0.41–1.13)0.83 (0.64–1.06)0.68 (0.41–1.13)0.141.08 (0.45–2.60)0.80 (0.58–1.11)0.64 (0.34–1.23)1.8E−05
Alcohol use disorderrs145649722G/CCLCN5Mayo0.04S0.78 (0.28–2.15)0.88 (0.53–1.47)0.78 (0.28–2.15)0.630.73 (0.16–3.29)0.92 (0.46–1.83)0.84 (0.21–3.36)0.88
GAIN0.05S2.60 (1.24–5.47)1.61 (1.11–2.34)2.60 (1.24–5.47)0.018.29 (2.50–27.51)0.58 (0.29–1.18)0.34 (0.08–1.39)4.1E−05
Meta S1.68 (0.92–3.05)1.30 (0.96–1.75)1.68 (0.92–3.05)0.093.20 (1.26–8.15)0.74 (0.45–1.21)0.55 (0.21–1.47)4.1E−04
  1. Odds ratios associated with an increase of one minor allele copy in men (ORM) or women (ORW1) or an increase of two copies in women (ORW2) are reported for two different analysis approaches. The XCI-informed approach employed a sex-adjusted logistic regression model (Eq. 1), but coded the SNP variable differently dependent on presumed XCI status (listed in the “Chosen XCI status” column). SNPs were assigned a status of subject (S) or escaping from inactivation, based on prior work on which regions of the X chromosome experience inactivation. For SNPs in regions of unknown XCI status (entries with asterisk in the “Chosen XCI status” column), presumed XCI status was determined by fitting the model using both the PLINK and Clayton coding schemes and using Akaike information criterion to select the more appropriate model. The XCI-robust approach employed a sex-adjusted logistic regression model with a SNP-sex interaction term (Eq. 2). The significance of the SNP and SNP-sex terms in the model was assessed by a χ2 test with two degrees-of-freedom (2df)
  2. Italics denote the results of the meta-analysis