DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=1.562e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_2L_t	0.01635
In_3R_Mo	0.06304

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	7.0218	0.0299
In_3R_Mo	5.4979	0.064

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2401 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	712399	3L_712399_SNP [dm3] 3L_712399_SNP [dm6]	A	T	7.692e^-7	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712385	3L_712385_DEL [dm3] 3L_712385_DEL [dm6]	TA	T	9.445e^-7	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	4094020	X_4094020_SNP [dm3] X_4199987_SNP [dm6]	T	C	1.135e^-6	0.333	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	712376	3L_712376_SNP [dm3] 3L_712376_SNP [dm6]	G	A	1.206e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	4737896	3L_4737896_SNP [dm3] 3L_4737896_SNP [dm6]	G	A	1.288e^-6	0.333	INTRON RhoGEF64C
3L	712423	3L_712423_SNP [dm3] 3L_712423_SNP [dm6]	G	C	1.322e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	3154188	X_3154188_SNP [dm3] X_3260155_SNP [dm6]	C	T	1.488e^-6	0.333	INTRON dnc
3L	712384	3L_712384_SNP [dm3] 3L_712384_SNP [dm6]	T	C	1.635e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712388	3L_712388_DEL [dm3] 3L_712388_DEL [dm6]	AAT	A	1.723e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	711790	3L_711790_SNP [dm3] 3L_711790_SNP [dm6]	A	T	2.105e^-6	0.333	UTR_5_PRIME CG13896	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3L	4737895	3L_4737895_SNP [dm3] 3L_4737895_SNP [dm6]	A	G	2.176e^-6	0.333	INTRON RhoGEF64C
3L	712348	3L_712348_SNP [dm3] 3L_712348_SNP [dm6]	G	T	2.308e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	13570329	3R_13570329_SNP [dm3] 3R_17744607_SNP [dm6]	A	C	2.610e^-6	0.333	INTRON TyrRII	TF binding site mE1_TFBS_cad
3R	3469607	3R_3469607_SNP [dm3] 3R_7643885_SNP [dm6]	C	T	3.074e^-6	0.333	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	16202334	3L_16202334_SNP [dm3] 3L_16209234_SNP [dm6]	A	T	3.247e^-6	0.333	INTERGENIC	TF binding site mE1_TFBS_cad
3L	712337	3L_712337_SNP [dm3] 3L_712337_SNP [dm6]	G	T	3.250e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	2646080	3L_2646080_SNP [dm3] 3L_2646080_SNP [dm6]	C	T	3.274e^-6	0.333	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	712235	3L_712235_SNP [dm3] 3L_712235_SNP [dm6]	C	T	3.283e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3L	8207850	3L_8207850_SNP [dm3] 3L_8214750_SNP [dm6]	T	C	3.451e^-6	0.333	UPSTREAM CG8012 INTERGENIC
3L	16202321	3L_16202321_SNP [dm3] 3L_16209221_SNP [dm6]	G	T	3.864e^-6	0.333	INTERGENIC	TF binding site mE1_TFBS_cad
3L	711857	3L_711857_SNP [dm3] 3L_711857_SNP [dm6]	A	C	4.120e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3L	712377	3L_712377_SNP [dm3] 3L_712377_SNP [dm6]	A	C	4.314e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712319	3L_712319_INS [dm3] 3L_712319_INS [dm6]	C	CA	4.381e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712342	3L_712342_SNP [dm3] 3L_712342_SNP [dm6]	A	T	4.381e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712335	3L_712335_SNP [dm3] 3L_712335_SNP [dm6]	T	A	4.438e^-6	0.333	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	4093930	X_4093930_SNP [dm3] X_4199897_SNP [dm6]	T	C	4.974e^-6	0.359	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	712455	3L_712455_SNP [dm3] 3L_712455_SNP [dm6]	C	T	5.310e^-6	0.369	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	5.660e^-6	0.369	INTRON CG17839
3L	712374	3L_712374_SNP [dm3] 3L_712374_SNP [dm6]	G	C	6.005e^-6	0.369	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	21160839	X_21160839_SNP [dm3] X_21289812_SNP [dm6]	T	C	6.234e^-6	0.369	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13506075	2R_13506075_SNP [dm3] 2R_17618570_SNP [dm6]	T	G	6.341e^-6	0.369	UPSTREAM CG44403 INTRON CG10936
3L	712226	3L_712226_SNP [dm3] 3L_712226_SNP [dm6]	C	A	6.437e^-6	0.369	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	6.613e^-6	0.369	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	6.696e^-6	0.369	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	10435085	3R_10435085_SNP [dm3] 3R_14609363_SNP [dm6]	G	T	7.130e^-6	0.373	UPSTREAM CG14853 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	4093939	X_4093939_SNP [dm3] X_4199906_SNP [dm6]	A	C	7.158e^-6	0.373	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	413912	3L_413912_SNP [dm3] 3L_413912_SNP [dm6]	C	T	7.374e^-6	0.374	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	16896011	3L_16896011_SNP [dm3] 3L_16902911_SNP [dm6]	A	T	7.923e^-6	0.379	NON_SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_chinmo
3L	14555445	3L_14555445_SNP [dm3] 3L_14562345_SNP [dm6]	A	T	8.220e^-6	0.379	INTRON CG34039	TF binding site mE1_TFBS_bab1 mE1_TFBS_ttk
3L	16202369	3L_16202369_SNP [dm3] 3L_16209269_SNP [dm6]	G	A	8.342e^-6	0.379	INTERGENIC	TF binding site mE1_TFBS_cad
3L	712323	3L_712323_SNP [dm3] 3L_712323_SNP [dm6]	T	A	8.391e^-6	0.379	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	2868309	3R_2868309_SNP [dm3] 3R_7042587_SNP [dm6]	G	A	8.500e^-6	0.379	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	8.910e^-6	0.388	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	15483333	3L_15483333_SNP [dm3] 3L_15490233_SNP [dm6]	T	C	9.497e^-6	0.398	INTERGENIC
3L	4737892	3L_4737892_SNP [dm3] 3L_4737892_SNP [dm6]	T	C	9.567e^-6	0.398	INTRON RhoGEF64C
3L	13487564	3L_13487564_SNP [dm3] 3L_13494464_SNP [dm6]	G	T	9.754e^-6	0.398	INTRON Tgi	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	1.020e^-5	0.4	INTERGENIC
2L	8447278	2L_8447278_SNP [dm3] 2L_8447278_SNP [dm6]	T	G	1.029e^-5	0.4	NON_SYNONYMOUS_CODING U26 UTR_3_PRIME U26	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	8447265	2L_8447265_SNP [dm3] 2L_8447265_SNP [dm6]	A	G	1.051e^-5	0.4	NON_SYNONYMOUS_CODING U26 UTR_3_PRIME U26	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	15483312	3L_15483312_SNP [dm3] 3L_15490212_SNP [dm6]	A	G	1.066e^-5	0.4	INTERGENIC
3L	712322	3L_712322_SNP [dm3] 3L_712322_SNP [dm6]	A	G	1.092e^-5	0.401	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	2645600	3L_2645600_SNP [dm3] 3L_2645600_SNP [dm6]	A	T	1.148e^-5	0.414	INTRON CG1143	TF binding site mE1_TFBS_cad
3R	24353994	3R_24353994_SNP [dm3] 3R_28528272_SNP [dm6]	G	A	1.266e^-5	0.448	NON_SYNONYMOUS_CODING Ppn	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	14815465	3L_14815465_SNP [dm3] 3L_14822365_SNP [dm6]	G	A	1.305e^-5	0.453	INTRON CG17839
3L	2645866	3L_2645866_SNP [dm3] 3L_2645866_SNP [dm6]	A	G	1.372e^-5	0.468	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	17894354	2R_17894354_SNP [dm3] 2R_22006849_SNP [dm6]	A	G	1.397e^-5	0.468	INTRON CG34370
2R	12116819	2R_12116819_SNP [dm3] 2R_16229314_SNP [dm6]	A	G	1.432e^-5	0.471	SYNONYMOUS_CODING Tsf3 UPSTREAM CG15701 INTRON CG15706	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	712343	3L_712343_SNP [dm3] 3L_712343_SNP [dm6]	A	C	1.458e^-5	0.471	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	20262267	X_20262267_SNP [dm3] X_20391240_SNP [dm6]	A	G	1.567e^-5	0.498	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16202346	3L_16202346_SNP [dm3] 3L_16209246_SNP [dm6]	C	T	1.689e^-5	0.523	INTERGENIC	TF binding site mE1_TFBS_cad
X	13136787	X_13136787_SNP [dm3] X_13242754_SNP [dm6]	C	T	1.701e^-5	0.523	INTRON mew	TF binding site BDTNP1_TFBS_da
2L	19841437	2L_19841437_SNP [dm3] 2L_19841437_SNP [dm6]	G	A	1.784e^-5	0.539	INTRON sick
3R	21341350	3R_21341350_SNP [dm3] 3R_25515628_SNP [dm6]	G	T	1.873e^-5	0.557	UPSTREAM msi INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	9287766	X_9287766_SNP [dm3] X_9393733_SNP [dm6]	T	C	1.974e^-5	0.569	INTRON mgl	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	13137038	X_13137038_SNP [dm3] X_13243005_SNP [dm6]	A	G	2.018e^-5	0.569	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	13137037	X_13137037_SNP [dm3] X_13243004_SNP [dm6]	C	T	2.036e^-5	0.569	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	2.056e^-5	0.569	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	10443026	X_10443026_SNP [dm3] X_10548993_SNP [dm6]	C	T	2.100e^-5	0.569	INTRON spri
3L	7296139	3L_7296139_DEL [dm3] 3L_7303039_DEL [dm6]	AA	A	2.125e^-5	0.569	INTRON unc-13-4A
3L	13557427	3L_13557427_INS [dm3] 3L_13564327_INS [dm6]	G	TA	2.155e^-5	0.569	INTRON bru-3
3L	13557430	3L_13557430_DEL [dm3] 3L_13564330_DEL [dm6]	GTTT	G	2.155e^-5	0.569	INTRON bru-3
3R	13600672	3R_13600672_SNP [dm3] 3R_17774950_SNP [dm6]	C	T	2.203e^-5	0.572	UTR_5_PRIME CG43102 INTRON CG43102	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	21896719	3R_21896719_SNP [dm3] 3R_26070997_SNP [dm6]	C	T	2.228e^-5	0.572	EXON CR44950
3R	20231859	3R_20231859_SNP [dm3] 3R_24406137_SNP [dm6]	A	C	2.302e^-5	0.573	INTRON nAChRalpha1
2R	6016574	2R_6016574_SNP [dm3] 2R_10129069_SNP [dm6]	G	A	2.330e^-5	0.573	INTRON gem	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	15483234	3L_15483234_SNP [dm3] 3L_15490134_SNP [dm6]	A	C	2.351e^-5	0.573	INTERGENIC
3R	13139524	3R_13139524_SNP [dm3] 3R_17313802_SNP [dm6]	G	T	2.353e^-5	0.573	INTERGENIC
3R	5709131	3R_5709131_SNP [dm3] 3R_9883409_SNP [dm6]	C	G	2.397e^-5	0.576	INTRON Glut4EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	376777	2L_376777_SNP [dm3] 2L_376777_SNP [dm6]	G	A	2.587e^-5	0.614	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
3R	12970762	3R_12970762_SNP [dm3] 3R_17145040_SNP [dm6]	A	T	2.687e^-5	0.627	UTR_3_PRIME m-cup DOWNSTREAM m-cup
3L	15483232	3L_15483232_SNP [dm3] 3L_15490132_SNP [dm6]	A	T	2.711e^-5	0.627	INTERGENIC
X	17948777	X_17948777_SNP [dm3] X_18054744_SNP [dm6]	G	A	2.869e^-5	0.656	INTRON Sh
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	2.986e^-5	0.661	INTERGENIC
2L	21921535	2L_21921535_SNP [dm3] 2L_21921535_SNP [dm6]	T	C	3.029e^-5	0.661	INTERGENIC
2R	9147422	2R_9147422_SNP [dm3] 2R_13259917_SNP [dm6]	A	T	3.034e^-5	0.661	UPSTREAM CG42319 INTERGENIC
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	3.058e^-5	0.661	INTERGENIC
3R	25570656	3R_25570656_SNP [dm3] 3R_29744934_SNP [dm6]	G	A	3.065e^-5	0.661	SYNONYMOUS_CODING CG7609 UPSTREAM IntS11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	14489497	3L_14489497_SNP [dm3] 3L_14496397_SNP [dm6]	T	A	3.106e^-5	0.662	INTRON bbg	TF binding site mE1_TFBS_cad
3L	5886015	3L_5886015_SNP [dm3] 3L_5892915_SNP [dm6]	C	G	3.253e^-5	0.671	INTERGENIC
3L	14489486	3L_14489486_SNP [dm3] 3L_14496386_SNP [dm6]	A	C	3.325e^-5	0.671	INTRON bbg	TF binding site mE1_TFBS_cad
3L	14489495	3L_14489495_SNP [dm3] 3L_14496395_SNP [dm6]	G	A	3.325e^-5	0.671	INTRON bbg	TF binding site mE1_TFBS_cad
3L	15483419	3L_15483419_SNP [dm3] 3L_15490319_SNP [dm6]	T	A	3.335e^-5	0.671	INTERGENIC
3R	5963561	3R_5963561_SNP [dm3] 3R_10137839_SNP [dm6]	T	C	3.363e^-5	0.671	INTRON tws	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	4342921	3R_4342921_SNP [dm3] 3R_8517199_SNP [dm6]	C	T	3.365e^-5	0.671	UPSTREAM CG11737 INTERGENIC
X	20215260	X_20215260_SNP [dm3] X_20344233_SNP [dm6]	A	C	3.564e^-5	0.7	INTERGENIC	transposable element FlyBase
2L	16759323	2L_16759323_SNP [dm3] 2L_16759323_SNP [dm6]	C	T	3.697e^-5	0.7	INTRON ppk17
X	17952250	X_17952250_SNP [dm3] X_18058217_SNP [dm6]	G	A	3.728e^-5	0.7	INTRON Sh
3L	7461509	3L_7461509_SNP [dm3] 3L_7468409_SNP [dm6]	G	T	3.744e^-5	0.7	UTR_3_PRIME CG42660 & 2 others
2L	16239804	2L_16239804_SNP [dm3] 2L_16239804_SNP [dm6]	C	T	3.748e^-5	0.7	INTRON CG42817
3L	4737859	3L_4737859_SNP [dm3] 3L_4737859_SNP [dm6]	A	G	3.755e^-5	0.7	INTRON RhoGEF64C

Showing 1 to 100 of 1,000 entries

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GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=9.698e^-3)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_2L_t	0.05846

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.5285	0.063
In_3R_K	4.6855	0.0961

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2137 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	2646080	3L_2646080_SNP [dm3] 3L_2646080_SNP [dm6]	C	T	1.495e^-7	0.28	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	21160839	X_21160839_SNP [dm3] X_21289812_SNP [dm6]	T	C	7.260e^-7	0.531	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	8.502e^-7	0.531	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13570329	3R_13570329_SNP [dm3] 3R_17744607_SNP [dm6]	A	C	1.456e^-6	0.654	INTRON TyrRII	TF binding site mE1_TFBS_cad
2R	9147422	2R_9147422_SNP [dm3] 2R_13259917_SNP [dm6]	A	T	1.887e^-6	0.654	UPSTREAM CG42319 INTERGENIC
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	2.093e^-6	0.654	INTERGENIC
2R	9147438	2R_9147438_SNP [dm3] 2R_13259933_SNP [dm6]	G	A	2.811e^-6	0.687	UPSTREAM CG42319 INTERGENIC
X	21063578	X_21063578_SNP [dm3] X_21192551_SNP [dm6]	G	A	2.931e^-6	0.687	UPSTREAM CG14579 INTERGENIC
2R	9147482	2R_9147482_SNP [dm3] 2R_13259977_SNP [dm6]	A	G	3.740e^-6	0.704	UPSTREAM CG42319 INTERGENIC
2R	9147435	2R_9147435_SNP [dm3] 2R_13259930_SNP [dm6]	T	A	4.123e^-6	0.704	UPSTREAM CG42319 INTERGENIC
3L	4737896	3L_4737896_SNP [dm3] 3L_4737896_SNP [dm6]	G	A	4.129e^-6	0.704	INTRON RhoGEF64C
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	6.155e^-6	0.714	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	2926031	X_2926031_SNP [dm3] X_3031998_SNP [dm6]	C	A	6.891e^-6	0.714	INTRON kirre
3L	4737895	3L_4737895_SNP [dm3] 3L_4737895_SNP [dm6]	A	G	6.957e^-6	0.714	INTRON RhoGEF64C
3R	21896719	3R_21896719_SNP [dm3] 3R_26070997_SNP [dm6]	C	T	7.215e^-6	0.714	EXON CR44950
2R	9134428	2R_9134428_SNP [dm3] 2R_13246923_SNP [dm6]	A	G	8.167e^-6	0.714	NON_SYNONYMOUS_CODING Mp20	TF binding site mE1_TFBS_cad
X	18464186	X_18464186_SNP [dm3] X_18570153_SNP [dm6]	C	A	8.880e^-6	0.714	INTRON Bx	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo
3R	27128046	3R_27128046_SNP [dm3] 3R_31302324_SNP [dm6]	C	T	9.015e^-6	0.714	DOWNSTREAM CG11340 INTERGENIC	TF binding site mE1_TFBS_inv
3L	5886015	3L_5886015_SNP [dm3] 3L_5892915_SNP [dm6]	C	G	9.406e^-6	0.714	INTERGENIC
2R	11330036	2R_11330036_SNP [dm3] 2R_15442531_SNP [dm6]	G	C	9.744e^-6	0.714	INTRON CG43729
2R	9147155	2R_9147155_SNP [dm3] 2R_13259650_SNP [dm6]	A	T	9.917e^-6	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
2R	11330161	2R_11330161_SNP [dm3] 2R_15442656_SNP [dm6]	G	A	1.047e^-5	0.714	INTRON CG43729
2R	11330066	2R_11330066_SNP [dm3] 2R_15442561_SNP [dm6]	G	T	1.151e^-5	0.714	INTRON CG43729
3L	6100247	3L_6100247_SNP [dm3] 3L_6107147_SNP [dm6]	C	T	1.198e^-5	0.714	INTRON Ets65A	TF binding site mE1_TFBS_cad
3L	6100199	3L_6100199_SNP [dm3] 3L_6107099_SNP [dm6]	C	T	1.272e^-5	0.714	INTRON Ets65A	TF binding site mE1_TFBS_cad
3R	25779128	3R_25779128_SNP [dm3] 3R_29953406_SNP [dm6]	G	A	1.277e^-5	0.714	SYNONYMOUS_CODING TkR99D
3L	3680402	3L_3680402_SNP [dm3] 3L_3680402_SNP [dm6]	T	C	1.289e^-5	0.714	INTERGENIC
X	4094020	X_4094020_SNP [dm3] X_4199987_SNP [dm6]	T	C	1.305e^-5	0.714	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	1.320e^-5	0.714	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	2645600	3L_2645600_SNP [dm3] 3L_2645600_SNP [dm6]	A	T	1.342e^-5	0.714	INTRON CG1143	TF binding site mE1_TFBS_cad
2R	13950559	2R_13950559_SNP [dm3] 2R_18063054_SNP [dm6]	A	T	1.408e^-5	0.714	INTRON CG34386
X	2926734	X_2926734_SNP [dm3] X_3032701_SNP [dm6]	C	A	1.416e^-5	0.714	INTRON kirre
2R	11330408	2R_11330408_SNP [dm3] 2R_15442903_SNP [dm6]	C	T	1.418e^-5	0.714	INTRON CG43729
3L	8391972	3L_8391972_SNP [dm3] 3L_8398872_SNP [dm6]	A	T	1.467e^-5	0.714	INTRON CG7120
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	1.478e^-5	0.714	INTRON CG17839
X	5115825	X_5115825_SNP [dm3] X_5221792_SNP [dm6]	A	G	1.483e^-5	0.714	INTRON CG15465 & 1 other
2L	7207197	2L_7207197_SNP [dm3] 2L_7207197_SNP [dm6]	A	G	1.588e^-5	0.714	SYNONYMOUS_CODING CG13784 UTR_3_PRIME CG13784	TF binding site mE1_TFBS_sens
3R	15213950	3R_15213950_SNP [dm3] 3R_19388228_SNP [dm6]	G	A	1.617e^-5	0.714	DOWNSTREAM CR34285 INTRON Ino80 & 1 other	TF binding site mE1_TFBS_sens
2L	15281202	2L_15281202_DEL [dm3] 2L_15281202_DEL [dm6]	CC	T	1.640e^-5	0.714	DOWNSTREAM CR45349 INTERGENIC
3L	7479975	3L_7479975_SNP [dm3] 3L_7486875_SNP [dm6]	T	C	1.650e^-5	0.714	SYNONYMOUS_CODING mthl6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11327929	2R_11327929_SNP [dm3] 2R_15440424_SNP [dm6]	G	T	1.727e^-5	0.714	INTRON CG43729
2R	9147038	2R_9147038_SNP [dm3] 2R_13259533_SNP [dm6]	G	A	1.818e^-5	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
X	12850971	X_12850971_SNP [dm3] X_12956938_SNP [dm6]	G	T	1.822e^-5	0.714	INTRON hec
2R	12696827	2R_12696827_SNP [dm3] 2R_16809322_SNP [dm6]	C	A	1.869e^-5	0.714	INTERGENIC
3R	18478641	3R_18478641_SNP [dm3] 3R_22652919_SNP [dm6]	G	T	1.882e^-5	0.714	INTRON CG45058	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9147009	2R_9147009_SNP [dm3] 2R_13259504_SNP [dm6]	T	G	1.908e^-5	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
3L	16202369	3L_16202369_SNP [dm3] 3L_16209269_SNP [dm6]	G	A	1.920e^-5	0.714	INTERGENIC	TF binding site mE1_TFBS_cad
3R	5145048	3R_5145048_SNP [dm3] 3R_9319326_SNP [dm6]	G	A	2.024e^-5	0.714	INTRON CG8861
X	4091100	X_4091100_SNP [dm3] X_4197067_SNP [dm6]	G	C	2.053e^-5	0.714	INTRON Fas2
2R	9147010	2R_9147010_SNP [dm3] 2R_13259505_SNP [dm6]	T	G	2.068e^-5	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
2R	20946369	2R_20946369_SNP [dm3] 2R_25058846_SNP [dm6]	C	T	2.220e^-5	0.714	INTERGENIC	regulatory region FlyBase REDfly_CRMs
2R	11330698	2R_11330698_SNP [dm3] 2R_15443193_SNP [dm6]	G	T	2.351e^-5	0.714	INTRON CG43729
X	5120460	X_5120460_SNP [dm3] X_5226427_SNP [dm6]	A	G	2.361e^-5	0.714	INTRON CG15465 & 1 other
3L	16202334	3L_16202334_SNP [dm3] 3L_16209234_SNP [dm6]	A	T	2.384e^-5	0.714	INTERGENIC	TF binding site mE1_TFBS_cad
2L	12260510	2L_12260510_SNP [dm3] 2L_12260510_SNP [dm6]	T	C	2.403e^-5	0.714	INTRON aret
3L	7480613	3L_7480613_SNP [dm3] 3L_7487513_SNP [dm6]	A	G	2.429e^-5	0.714	INTRON mthl6
3L	2644981	3L_2644981_SNP [dm3] 3L_2644981_SNP [dm6]	A	T	2.471e^-5	0.714	UPSTREAM CG1143 INTERGENIC
3R	26618148	3R_26618148_SNP [dm3] 3R_30792426_SNP [dm6]	T	G	2.510e^-5	0.714	SYNONYMOUS_CODING wts UPSTREAM mir-1013	TF binding site mE1_TFBS_sens
X	4091094	X_4091094_DEL [dm3] X_4197061_DEL [dm6]	AAA	A	2.613e^-5	0.714	INTRON Fas2
2L	4512888	2L_4512888_SNP [dm3] 2L_4512888_SNP [dm6]	G	A	2.640e^-5	0.714	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11728415	3L_11728415_SNP [dm3] 3L_11735315_SNP [dm6]	C	T	2.758e^-5	0.714	UTR_3_PRIME CG6024 DOWNSTREAM CG6024
3R	12971257	3R_12971257_SNP [dm3] 3R_17145535_SNP [dm6]	A	C	2.775e^-5	0.714	UTR_3_PRIME m-cup	TF binding site mE1_TFBS_cad
3R	12971260	3R_12971260_DEL [dm3] 3R_17145538_DEL [dm6]	AGGTAAGCATCCTA...	G	2.775e^-5	0.714	UTR_3_PRIME m-cup	TF binding site mE1_TFBS_cad
3L	16202321	3L_16202321_SNP [dm3] 3L_16209221_SNP [dm6]	G	T	2.812e^-5	0.714	INTERGENIC	TF binding site mE1_TFBS_cad
3L	712348	3L_712348_SNP [dm3] 3L_712348_SNP [dm6]	G	T	2.818e^-5	0.714	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
2R	18418701	2R_18418701_SNP [dm3] 2R_22531196_SNP [dm6]	A	C	2.825e^-5	0.714	INTRON px
2R	18418702	2R_18418702_SNP [dm3] 2R_22531197_SNP [dm6]	C	A	2.825e^-5	0.714	INTRON px
3L	7777439	3L_7777439_SNP [dm3] 3L_7784339_SNP [dm6]	C	T	2.870e^-5	0.714	INTRON CG32369
3L	7072423	3L_7072423_SNP [dm3] 3L_7079323_SNP [dm6]	C	A	2.922e^-5	0.714	INTERGENIC
2R	9147034	2R_9147034_SNP [dm3] 2R_13259529_SNP [dm6]	G	T	3.030e^-5	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
2L	12896052	2L_12896052_SNP [dm3] 2L_12896052_SNP [dm6]	T	C	3.052e^-5	0.714	INTERGENIC
3L	11599845	3L_11599845_SNP [dm3] 3L_11606745_SNP [dm6]	T	C	3.053e^-5	0.714	SYNONYMOUS_CODING CG6091
3L	8391974	3L_8391974_SNP [dm3] 3L_8398874_SNP [dm6]	G	A	3.093e^-5	0.714	INTRON CG7120
X	18463732	X_18463732_SNP [dm3] X_18569699_SNP [dm6]	A	G	3.094e^-5	0.714	INTRON Bx	TF binding site BDTNP1_TFBS_da
2R	11327910	2R_11327910_SNP [dm3] 2R_15440405_SNP [dm6]	T	C	3.134e^-5	0.714	INTRON CG43729
3R	2868309	3R_2868309_SNP [dm3] 3R_7042587_SNP [dm6]	G	A	3.148e^-5	0.714	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	5709131	3R_5709131_SNP [dm3] 3R_9883409_SNP [dm6]	C	G	3.200e^-5	0.714	INTRON Glut4EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14561384	3L_14561384_SNP [dm3] 3L_14568284_SNP [dm6]	G	A	3.212e^-5	0.714	DOWNSTREAM CG42758 INTERGENIC
2L	7365708	2L_7365708_SNP [dm3] 2L_7365708_SNP [dm6]	C	T	3.284e^-5	0.714	INTRON Wnt10
3R	5137887	3R_5137887_SNP [dm3] 3R_9312165_SNP [dm6]	A	G	3.286e^-5	0.714	INTRON CG8861
3L	4534444	3L_4534444_SNP [dm3] 3L_4534444_SNP [dm6]	C	A	3.291e^-5	0.714	INTRON CG11353
X	10543785	X_10543785_SNP [dm3] X_10649752_SNP [dm6]	T	C	3.301e^-5	0.714	INTRON X11Lbeta
X	14154319	X_14154319_SNP [dm3] X_14260286_SNP [dm6]	G	C	3.307e^-5	0.714	UPSTREAM CG1461 INTERGENIC
3L	16983394	3L_16983394_SNP [dm3] 3L_16990294_SNP [dm6]	C	A	3.414e^-5	0.714	INTRON Exn
3L	14057292	3L_14057292_SNP [dm3] 3L_14064192_SNP [dm6]	C	T	3.432e^-5	0.714	INTRON CG32138	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	11330331	2R_11330331_SNP [dm3] 2R_15442826_SNP [dm6]	A	G	3.462e^-5	0.714	INTRON CG43729
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	3.492e^-5	0.714	INTERGENIC
3L	2646601	3L_2646601_SNP [dm3] 3L_2646601_SNP [dm6]	T	C	3.564e^-5	0.714	UTR_3_PRIME CG1143	TF binding site mE1_TFBS_cad
3L	14815465	3L_14815465_SNP [dm3] 3L_14822365_SNP [dm6]	G	A	3.578e^-5	0.714	INTRON CG17839
X	13136787	X_13136787_SNP [dm3] X_13242754_SNP [dm6]	C	T	3.594e^-5	0.714	INTRON mew	TF binding site BDTNP1_TFBS_da
2R	9147026	2R_9147026_SNP [dm3] 2R_13259521_SNP [dm6]	T	A	3.642e^-5	0.714	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
2R	13415564	2R_13415564_SNP [dm3] 2R_17528059_SNP [dm6]	G	A	3.658e^-5	0.714	SYNONYMOUS_CODING Patronin
2R	12282058	2R_12282058_SNP [dm3] 2R_16394553_SNP [dm6]	G	A	3.691e^-5	0.714	INTRON Sema-2b
3L	6100265	3L_6100265_SNP [dm3] 3L_6107165_SNP [dm6]	C	T	3.760e^-5	0.714	INTRON Ets65A	TF binding site mE1_TFBS_cad
X	8402577	X_8402577_SNP [dm3] X_8508544_SNP [dm6]	G	A	3.773e^-5	0.714	INTRON CG33181
2L	2922161	2L_2922161_SNP [dm3] 2L_2922161_SNP [dm6]	T	A	3.797e^-5	0.714	INTRON lilli
3L	12450024	3L_12450024_SNP [dm3] 3L_12456924_SNP [dm6]	G	A	3.813e^-5	0.714	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3L	4737859	3L_4737859_SNP [dm3] 3L_4737859_SNP [dm6]	A	G	3.816e^-5	0.714	INTRON RhoGEF64C
3L	14555445	3L_14555445_SNP [dm3] 3L_14562345_SNP [dm6]	A	T	3.825e^-5	0.714	INTRON CG34039	TF binding site mE1_TFBS_bab1 mE1_TFBS_ttk
2L	8619047	2L_8619047_SNP [dm3] 2L_8619047_SNP [dm6]	C	T	3.835e^-5	0.714	UPSTREAM tRNA:CR31602 INTRON Sema-1a

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By genomic position
Variant impact
Gene name

Wing_Area phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results