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=1.096e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2332 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	9337999	2L_9337999_SNP [dm3] 2L_9337999_SNP [dm6]	T	C	2.637e^-7	0.332	SPLICE_SITE_REGION Eaat1 INTRON Eaat1
2L	9337986	2L_9337986_SNP [dm3] 2L_9337986_SNP [dm6]	A	C	3.546e^-7	0.332	INTRON Eaat1
X	16918901	X_16918901_SNP [dm3] X_17024868_SNP [dm6]	G	C	9.363e^-7	0.462	DOWNSTREAM CG43997 INTRON CG45002
X	17715695	X_17715695_SNP [dm3] X_17821662_SNP [dm6]	C	T	1.288e^-6	0.462	UTR_3_PRIME Socs16D	TF binding site BDTNP1_TFBS_dl mE1_TFBS_kn
X	17715708	X_17715708_DEL [dm3] X_17821675_DEL [dm6]	TGTTACT	T	1.447e^-6	0.462	UTR_3_PRIME Socs16D	TF binding site BDTNP1_TFBS_dl mE1_TFBS_kn
2R	19085373	2R_19085373_SNP [dm3] 2R_23197850_SNP [dm6]	T	G	1.704e^-6	0.462	INTRON CG34371
2R	9127159	2R_9127159_SNP [dm3] 2R_13239654_SNP [dm6]	T	A	2.067e^-6	0.462	UPSTREAM GstE14 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
3L	10697136	3L_10697136_DEL [dm3] 3L_10704036_DEL [dm6]	TT	T	2.371e^-6	0.462	INTERGENIC
2R	9127115	2R_9127115_SNP [dm3] 2R_13239610_SNP [dm6]	A	C	3.135e^-6	0.462	UPSTREAM GstE14 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
X	17715730	X_17715730_SNP [dm3] X_17821697_SNP [dm6]	T	A	3.219e^-6	0.462	UTR_3_PRIME Socs16D
2L	9337938	2L_9337938_SNP [dm3] 2L_9337938_SNP [dm6]	T	A	3.524e^-6	0.462	INTRON Eaat1
2R	19317385	2R_19317385_SNP [dm3] 2R_23429862_SNP [dm6]	A	G	3.715e^-6	0.462	INTRON CG9815
3L	10697113	3L_10697113_SNP [dm3] 3L_10704013_SNP [dm6]	A	C	3.802e^-6	0.462	INTERGENIC
2L	15990382	2L_15990382_SNP [dm3] 2L_15990382_SNP [dm6]	A	T	4.138e^-6	0.462	DOWNSTREAM CR43412 INTERGENIC
2L	1070360	2L_1070360_SNP [dm3] 2L_1070360_SNP [dm6]	G	A	4.325e^-6	0.462	INTRON S	TF binding site mE1_TFBS_cad
2L	9337929	2L_9337929_SNP [dm3] 2L_9337929_SNP [dm6]	T	C	4.915e^-6	0.462	UTR_5_PRIME Eaat1 INTRON Eaat1
3L	9433547	3L_9433547_SNP [dm3] 3L_9440447_SNP [dm6]	A	C	4.955e^-6	0.462	UTR_3_PRIME Nf-YA DOWNSTREAM MTF-1 INTRON Bet3
3L	10697056	3L_10697056_SNP [dm3] 3L_10703956_SNP [dm6]	A	T	5.000e^-6	0.462	INTERGENIC
3R	24184710	3R_24184710_SNP [dm3] 3R_28358988_SNP [dm6]	T	G	5.019e^-6	0.462	INTERGENIC
3R	8080148	3R_8080148_SNP [dm3] 3R_12254426_SNP [dm6]	T	C	5.693e^-6	0.462	SYNONYMOUS_CODING CG3942	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	5688365	3R_5688365_SNP [dm3] 3R_9862643_SNP [dm6]	A	G	5.707e^-6	0.462	INTRON Teh1
2L	11195016	2L_11195016_SNP [dm3] 2L_11195016_SNP [dm6]	T	C	5.913e^-6	0.462	INTRON Ca-beta	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_inv
2L	9337981	2L_9337981_SNP [dm3] 2L_9337981_SNP [dm6]	C	A	6.080e^-6	0.462	INTRON Eaat1
3R	24184039	3R_24184039_SNP [dm3] 3R_28358317_SNP [dm6]	A	T	6.183e^-6	0.462	INTERGENIC
3R	13366999	3R_13366999_SNP [dm3] 3R_17541277_SNP [dm6]	A	G	6.404e^-6	0.462	NON_SYNONYMOUS_CODING SF1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	8938390	2R_8938390_SNP [dm3] 2R_13050885_SNP [dm6]	G	A	6.899e^-6	0.462	INTERGENIC
2L	9337953	2L_9337953_DEL [dm3] 2L_9337953_DEL [dm6]	AAACAAATAGATTCTATTAT...	A	7.021e^-6	0.462	INTRON Eaat1
X	16516033	X_16516033_SNP [dm3] X_16622000_SNP [dm6]	A	T	7.098e^-6	0.462	UPSTREAM CG9782 INTERGENIC
2L	9337952	2L_9337952_SNP [dm3] 2L_9337952_SNP [dm6]	G	T	7.142e^-6	0.462	INTRON Eaat1
2R	5980207	2R_5980207_SNP [dm3] 2R_10092702_SNP [dm6]	C	G	7.615e^-6	0.476	INTRON CG2269
X	21960760	X_21960760_SNP [dm3] X_22558924_SNP [dm6]	T	C	7.879e^-6	0.476	INTERGENIC	transposable element FlyBase
2L	9337927	2L_9337927_SNP [dm3] 2L_9337927_SNP [dm6]	A	G	8.946e^-6	0.524	UTR_5_PRIME Eaat1 INTRON Eaat1
2L	15990388	2L_15990388_SNP [dm3] 2L_15990388_SNP [dm6]	A	G	9.937e^-6	0.564	DOWNSTREAM CR43412 INTERGENIC
2R	3257491	2R_3257491_SNP [dm3] 2R_7369986_SNP [dm6]	T	C	1.040e^-5	0.573	INTRON Dscam1
2R	8724176	2R_8724176_SNP [dm3] 2R_12836671_SNP [dm6]	C	T	1.127e^-5	0.578	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	16899126	X_16899126_SNP [dm3] X_17005093_SNP [dm6]	G	A	1.210e^-5	0.578	INTRON CG45002
3L	15705645	3L_15705645_SNP [dm3] 3L_15712545_SNP [dm6]	G	T	1.255e^-5	0.578	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Stat92E
3L	10697153	3L_10697153_SNP [dm3] 3L_10704053_SNP [dm6]	C	T	1.272e^-5	0.578	INTERGENIC
2R	8937359	2R_8937359_SNP [dm3] 2R_13049854_SNP [dm6]	C	T	1.292e^-5	0.578	UPSTREAM CG13324 INTERGENIC
2R	8937376	2R_8937376_SNP [dm3] 2R_13049871_SNP [dm6]	A	T	1.292e^-5	0.578	UPSTREAM CG13324 INTERGENIC
2R	8937487	2R_8937487_SNP [dm3] 2R_13049982_SNP [dm6]	C	T	1.292e^-5	0.578	UPSTREAM CG13324 INTERGENIC
2R	9127105	2R_9127105_SNP [dm3] 2R_13239600_SNP [dm6]	A	G	1.352e^-5	0.578	UPSTREAM GstE14 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
3L	11823406	3L_11823406_SNP [dm3] 3L_11830306_SNP [dm6]	G	A	1.398e^-5	0.578	SYNONYMOUS_CODING CG7264 INTRON CycA	TF binding site mE1_TFBS_sens
3L	11526225	3L_11526225_SNP [dm3] 3L_11533125_SNP [dm6]	C	T	1.403e^-5	0.578	INTRON Mob2
X	6934656	X_6934656_SNP [dm3] X_7040623_SNP [dm6]	G	A	1.406e^-5	0.578	UTR_5_PRIME CG14427 INTRON CG12541	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3R	6404817	3R_6404817_SNP [dm3] 3R_10579095_SNP [dm6]	A	C	1.418e^-5	0.578	INTRON hth	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA
2R	10007632	2R_10007632_SNP [dm3] 2R_14120127_SNP [dm6]	T	A	1.486e^-5	0.593	INTRON Prosap	TF binding site mE1_TFBS_HSA
3R	12512612	3R_12512612_SNP [dm3] 3R_16686890_SNP [dm6]	A	T	1.538e^-5	0.6	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	16231331	X_16231331_SNP [dm3] X_16337298_SNP [dm6]	A	C	1.641e^-5	0.619	INTRON Dsp1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	3257580	2R_3257580_SNP [dm3] 2R_7370075_SNP [dm6]	T	C	1.651e^-5	0.619	INTRON Dscam1
3R	20103360	3R_20103360_SNP [dm3] 3R_24277638_SNP [dm6]	C	A	1.780e^-5	0.639	NON_SYNONYMOUS_CODING Orct	TF binding site mE1_TFBS_chinmo
3L	4270024	3L_4270024_SNP [dm3] 3L_4270024_SNP [dm6]	A	T	1.816e^-5	0.639	INTRON CG1273	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	4270079	3L_4270079_SNP [dm3] 3L_4270079_SNP [dm6]	T	A	1.816e^-5	0.639	INTRON CG1273	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	2513159	3L_2513159_SNP [dm3] 3L_2513159_SNP [dm6]	G	A	1.872e^-5	0.639	INTRON Spn	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	13264175	3R_13264175_SNP [dm3] 3R_17438453_SNP [dm6]	T	C	1.875e^-5	0.639	DOWNSTREAM CG14331 INTRON CG5873
2R	3257560	2R_3257560_SNP [dm3] 2R_7370055_SNP [dm6]	C	T	1.928e^-5	0.645	INTRON Dscam1
X	16899139	X_16899139_SNP [dm3] X_17005106_SNP [dm6]	A	T	2.061e^-5	0.648	INTRON CG45002
2R	10580177	2R_10580177_SNP [dm3] 2R_14692672_SNP [dm6]	A	G	2.078e^-5	0.648	INTRON mspo
3L	19205114	3L_19205114_SNP [dm3] 3L_19212014_SNP [dm6]	A	T	2.121e^-5	0.648	INTRON fz2
3R	13374051	3R_13374051_SNP [dm3] 3R_17548329_SNP [dm6]	T	C	2.194e^-5	0.648	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12764153	2R_12764153_SNP [dm3] 2R_16876648_SNP [dm6]	C	T	2.204e^-5	0.648	NON_SYNONYMOUS_CODING CG8910	TF binding site mE1_TFBS_chinmo
X	20217270	X_20217270_SNP [dm3] X_20346243_SNP [dm6]	A	C	2.205e^-5	0.648	INTERGENIC
2L	11397732	2L_11397732_SNP [dm3] 2L_11397732_SNP [dm6]	A	T	2.206e^-5	0.648	INTERGENIC	regulatory region REDfly_CRMs
3L	15705781	3L_15705781_DEL [dm3] 3L_15712681_DEL [dm6]	GCGAAA	G	2.236e^-5	0.648	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Stat92E
2R	19085368	2R_19085368_DEL [dm3] 2R_23197845_DEL [dm6]	GG	G	2.247e^-5	0.648	INTRON CG34371
2R	16764348	2R_16764348_SNP [dm3] 2R_20876843_SNP [dm6]	T	C	2.298e^-5	0.652	INTRON Ipk1
X	16130895	X_16130895_SNP [dm3] X_16236862_SNP [dm6]	T	A	2.333e^-5	0.653	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_Kr
X	13321820	X_13321820_SNP [dm3] X_13427787_SNP [dm6]	G	T	2.376e^-5	0.655	INTERGENIC	TF binding site mE1_TFBS_inv
3L	12015931	3L_12015931_SNP [dm3] 3L_12022831_SNP [dm6]	T	C	2.426e^-5	0.655	INTRON rols
X	20734893	X_20734893_INS [dm3] X_20863866_INS [dm6]	T	TAGATT	2.459e^-5	0.655	UPSTREAM CG43193 INTRON shakB
X	16899150	X_16899150_DEL [dm3] X_17005117_DEL [dm6]	CACATGC	C	2.533e^-5	0.655	INTRON CG45002
2R	8938960	2R_8938960_DEL [dm3] 2R_13051455_DEL [dm6]	TT	T	2.548e^-5	0.655	INTERGENIC
2R	15281301	2R_15281301_SNP [dm3] 2R_19393796_SNP [dm6]	G	A	2.553e^-5	0.655	SYNONYMOUS_CODING SdhA	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	10053109	3R_10053109_SNP [dm3] 3R_14227387_SNP [dm6]	A	T	2.645e^-5	0.67	UPSTREAM CG9631 DOWNSTREAM CG9624 INTERGENIC
2L	13413679	2L_13413679_SNP [dm3] 2L_13413679_SNP [dm6]	G	A	2.753e^-5	0.68	UTR_3_PRIME CG16848 DOWNSTREAM CG16956
3R	13959851	3R_13959851_SNP [dm3] 3R_18134129_SNP [dm6]	T	A	2.779e^-5	0.68	UTR_3_PRIME sr DOWNSTREAM sr
2L	1165333	2L_1165333_SNP [dm3] 2L_1165333_SNP [dm6]	T	C	2.793e^-5	0.68	NON_SYNONYMOUS_CODING IntS14	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	18508942	2L_18508942_DEL [dm3] 2L_18508942_DEL [dm6]	TAGGGGG	T	2.942e^-5	0.707	UPSTREAM CG10178 INTERGENIC
3R	13264347	3R_13264347_SNP [dm3] 3R_17438625_SNP [dm6]	T	C	3.021e^-5	0.709	DOWNSTREAM CG14331 INTRON CG5873
3L	15705789	3L_15705789_SNP [dm3] 3L_15712689_SNP [dm6]	T	A	3.072e^-5	0.709	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Stat92E
2R	8938969	2R_8938969_SNP [dm3] 2R_13051464_SNP [dm6]	A	C	3.077e^-5	0.709	INTERGENIC
X	9846610	X_9846610_SNP [dm3] X_9952577_SNP [dm6]	G	T	3.104e^-5	0.709	INTERGENIC
X	16899211	X_16899211_SNP [dm3] X_17005178_SNP [dm6]	A	G	3.148e^-5	0.71	INTRON CG45002
3R	12860093	3R_12860093_DEL [dm3] 3R_17034371_DEL [dm6]	TGATCT	A	3.244e^-5	0.71	DOWNSTREAM CG31268 INTRON CG4009	TF binding site mE1_TFBS_HSA
2R	3507859	2R_3507859_SNP [dm3] 2R_7620354_SNP [dm6]	C	T	3.287e^-5	0.71	UTR_5_PRIME CG1358	TF binding site mE1_TFBS_chinmo
2L	1956654	2L_1956654_SNP [dm3] 2L_1956654_SNP [dm6]	C	T	3.297e^-5	0.71	INTRON erm	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	10665197	3L_10665197_SNP [dm3] 3L_10672097_SNP [dm6]	G	T	3.330e^-5	0.71	INTRON simj	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	13951362	2L_13951362_SNP [dm3] 2L_13951362_SNP [dm6]	A	C	3.331e^-5	0.71	INTRON Ance-3
2L	908104	2L_908104_SNP [dm3] 2L_908104_SNP [dm6]	G	T	3.476e^-5	0.726	INTERGENIC
3R	24098443	3R_24098443_SNP [dm3] 3R_28272721_SNP [dm6]	C	G	3.487e^-5	0.726	INTERGENIC
3L	4211889	3L_4211889_SNP [dm3] 3L_4211889_SNP [dm6]	C	G	3.576e^-5	0.729	UPSTREAM Cpr64Ab DOWNSTREAM Cpr64Ac INTRON CG43367	TF binding site mE1_TFBS_cad
3R	24186904	3R_24186904_SNP [dm3] 3R_28361182_SNP [dm6]	A	T	3.577e^-5	0.729	INTERGENIC
3R	10053098	3R_10053098_SNP [dm3] 3R_14227376_SNP [dm6]	G	T	3.664e^-5	0.739	UPSTREAM CG9631 DOWNSTREAM CG9624 INTERGENIC
3L	9433633	3L_9433633_SNP [dm3] 3L_9440533_SNP [dm6]	T	C	3.760e^-5	0.75	UTR_3_PRIME Nf-YA INTRON Bet3
2R	10111074	2R_10111074_SNP [dm3] 2R_14223569_SNP [dm6]	T	C	3.855e^-5	0.757	INTRON CG8468	TF binding site BDTNP1_TFBS_twi
2R	3257836	2R_3257836_SNP [dm3] 2R_7370331_SNP [dm6]	T	G	3.892e^-5	0.757	INTRON Dscam1	regulatory region REDfly_CRMs
2R	17030247	2R_17030247_SNP [dm3] 2R_21142742_SNP [dm6]	G	C	3.962e^-5	0.757	SYNONYMOUS_CODING CG9406 UPSTREAM Magi & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	10580250	2R_10580250_SNP [dm3] 2R_14692745_SNP [dm6]	T	G	3.988e^-5	0.757	INTRON mspo
2L	1054577	2L_1054577_SNP [dm3] 2L_1054577_SNP [dm6]	T	A	4.048e^-5	0.757	INTRON S	TF binding site BDTNP1_TFBS_twi
X	16230647	X_16230647_SNP [dm3] X_16336614_SNP [dm6]	C	T	4.074e^-5	0.757	SYNONYMOUS_CODING Dsp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
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PC1_Nutri_Score_High phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results