Hub : Traits

pavca_ny_levercs_d4d5

Pavlovian Conditioned Approach, Sign-tracking, average lever contact number on days 4 and 5 of testing

Project: p50_paul_meyer_2014

242 significantly associated models · 59 unique genes

Significant Loci

#	chr	p0	p1	# assoc genes	# joint models	best TWAS P	best SNP P	cond SNP P	% var exp	joint genes
1	1	149862595	157827195	58	8	7.4e-10	1.9e-09	1.00	100	Aamdc B3gnt6 Emsy Dgat2 Plekhb1 Arap1 Clpb Mogat2
2	5	74868378	76264539	1	1	2.6e-07	4.4e-02	0.02	-34	RGD1566134

p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.

Pleiotropic Associations

Trait	chisq ratio	# genes⁺	# genes⁺⁺	% genes⁺⁺	corr	corr P	genes
retroperitoneal_fat_g	5.4	25	2	22	-0.99	5.3e-54	Aamdc Capn5 B3gnt6 Emsy Uvrag Dgat2 Lipt2 Pgm2l1 P4ha3 Ucp2 Dnajb13 Slco2b1 Mrpl48 Plekhb1 Fam168a P2ry6 Rsf1 Relt Mogat2 Tsku Gdpd5 Acer3 AABR07004881.1 Thap12 Coa4
dissection: PC 3 of all traits	6.5	9	0	0	-1.00	8.7e-23	Art2b Folr2 Anapc15 Rnf121 Trpc2 Nup98 Pgap2 Stim1 Trim68
reaction_time_meanrt_slope	14.2	1	0	0	0.00	1.0e+00	RGD1566134
pavca_ny_d2_magazine_cs	15.7	1	0	0	0.00	1.0e+00	RGD1566134
Total sessions with >9 infusions	15.1	1	0	0	0.00	1.0e+00	RGD1566134
crf_mi_active_responses	13.3	1	0	0	0.00	1.0e+00	RGD1566134
tautz: manual_mpc7	23.4	1	1	11	0.00	1.0e+00	RGD1566134
tautz: manual_mpc5	12.3	1	0	0	0.00	1.0e+00	RGD1566134
tautz: manual_mpc12	9.5	1	0	0	0.00	1.0e+00	RGD1566134
tautz: manual_spc24	27.7	1	1	11	0.00	1.0e+00	RGD1566134
tautz: manual_spc4	17.5	1	0	0	0.00	1.0e+00	RGD1566134
tautz: manual_spc6	11.4	1	0	0	0.00	1.0e+00	RGD1566134
tautz: manual_spc5	32.5	1	1	11	0.00	1.0e+00	RGD1566134
tautz: manual_mpc6	24.2	1	1	11	0.00	1.0e+00	RGD1566134
Liver zinc concentration	15.1	1	0	0	0.00	1.0e+00	RGD1566134
Liver sodium concentration	15.7	1	0	0	0.00	1.0e+00	RGD1566134

chisq ratio: Average Chi² statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes⁺: Shared significant genes at Bonferroni correction. # genes⁺⁺: Shared significant genes at transcriptome-wide significance. % genes⁺⁺: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.

Associations by panel

tissue	modality	# hits	% hits/tests	avg chisq
Adipose	alternative polyA	12	0.566	1.5
Adipose	alternative TSS	6	0.372	1.5
Adipose	gene expression	14	0.169	1.4
Adipose	isoform ratio	4	0.142	1.4
Adipose	intron excision ratio	5	0.171	1.3
Adipose	mRNA stability	8	0.232	1.5
BLA	alternative polyA	1	0.083	1.5
BLA	alternative TSS	4	0.475	1.6
BLA	gene expression	12	0.198	1.4
BLA	isoform ratio	0	0.000	1.3
BLA	intron excision ratio	3	0.100	1.3
BLA	mRNA stability	3	0.148	1.4
Brain	alternative polyA	3	0.150	1.5
Brain	alternative TSS	4	0.233	1.3
Brain	gene expression	14	0.155	1.4
Brain	isoform ratio	5	0.158	1.4
Brain	intron excision ratio	5	0.093	1.4
Brain	mRNA stability	9	0.206	1.4
Eye	alternative polyA	0	0.000	1.3
Eye	alternative TSS	1	0.417	1.5
Eye	gene expression	1	0.089	1.4
Eye	isoform ratio	0	0.000	1.6
Eye	intron excision ratio	1	0.163	1.5
Eye	mRNA stability	1	0.429	1.7
IL	alternative polyA	0	0.000	1.4
IL	alternative TSS	0	0.000	1.0
IL	gene expression	8	0.219	1.4
IL	isoform ratio	0	0.000	1.3
IL	intron excision ratio	1	0.104	1.4
IL	mRNA stability	0	0.000	1.3
LHb	alternative polyA	0	0.000	1.4
LHb	alternative TSS	0	0.000	1.2
LHb	gene expression	2	0.062	1.4
LHb	isoform ratio	0	0.000	1.3
LHb	intron excision ratio	0	0.000	1.4
LHb	mRNA stability	0	0.000	1.3
Liver	alternative polyA	6	0.399	1.6
Liver	alternative TSS	5	0.329	1.5
Liver	gene expression	15	0.209	1.4
Liver	isoform ratio	3	0.125	1.4
Liver	intron excision ratio	12	0.274	1.4
Liver	mRNA stability	7	0.285	1.4
NAcc	alternative polyA	1	0.192	1.4
NAcc	alternative TSS	0	0.000	1.0
NAcc	gene expression	4	0.122	1.4
NAcc	isoform ratio	0	0.000	1.3
NAcc	intron excision ratio	2	0.210	1.5
NAcc	mRNA stability	2	0.185	1.5
NAcc2	alternative polyA	0	0.000	1.5
NAcc2	alternative TSS	2	0.273	1.3
NAcc2	gene expression	9	0.169	1.4
NAcc2	isoform ratio	0	0.000	1.4
NAcc2	intron excision ratio	4	0.151	1.3
NAcc2	mRNA stability	7	0.392	1.5
OFC	alternative polyA	0	0.000	1.5
OFC	alternative TSS	0	0.000	1.1
OFC	gene expression	2	0.054	1.4
OFC	isoform ratio	1	0.123	1.4
OFC	intron excision ratio	0	0.000	1.3
OFC	mRNA stability	1	0.093	1.5
PL	alternative polyA	0	0.000	1.3
PL	alternative TSS	0	0.000	1.4
PL	gene expression	8	0.215	1.4
PL	isoform ratio	0	0.000	1.2
PL	intron excision ratio	0	0.000	1.3
PL	mRNA stability	0	0.000	1.4
PL2	alternative polyA	0	0.000	1.5
PL2	alternative TSS	2	0.213	1.3
PL2	gene expression	11	0.172	1.4
PL2	isoform ratio	1	0.054	1.4
PL2	intron excision ratio	2	0.063	1.4
PL2	mRNA stability	8	0.328	1.5

avg chisq: Average Chi² (squared Z-score) across all models in this panel for this trait.