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=9.320e^-2)
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

1611 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
X	14554233	X_14554233_INS [dm3] X_14660200_INS [dm6]	A	ACATA	5.529e^-7	1	INTERGENIC
X	10856569	X_10856569_SNP [dm3] X_10962536_SNP [dm6]	T	G	3.745e^-6	1	SYNONYMOUS_CODING Myo10A	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8941803	2R_8941803_SNP [dm3] 2R_13054298_SNP [dm6]	A	C	4.467e^-6	1	DOWNSTREAM Drl-2 INTERGENIC
X	12344731	X_12344731_SNP [dm3] X_12450698_SNP [dm6]	G	T	4.728e^-6	1	INTRON Pkcdelta
2R	8941801	2R_8941801_SNP [dm3] 2R_13054296_SNP [dm6]	G	A	4.746e^-6	1	DOWNSTREAM Drl-2 INTERGENIC
2L	18455346	2L_18455346_INS [dm3] 2L_18455346_INS [dm6]	A	AC	4.754e^-6	1	UTR_3_PRIME Ntf-2r UPSTREAM bsf & 1 other	TF binding site BDTNP1_TFBS_dl
2L	10980755	2L_10980755_SNP [dm3] 2L_10980755_SNP [dm6]	G	A	5.543e^-6	1	SYNONYMOUS_CODING SCAR	TF binding site mE1_TFBS_cad
2R	19519131	2R_19519131_SNP [dm3] 2R_23631608_SNP [dm6]	G	A	6.217e^-6	1	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl
X	10856533	X_10856533_SNP [dm3] X_10962500_SNP [dm6]	C	A	7.365e^-6	1	SYNONYMOUS_CODING Myo10A	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6980491	3R_6980491_SNP [dm3] 3R_11154769_SNP [dm6]	T	G	8.225e^-6	1	NON_SYNONYMOUS_CODING Ugt86Dc UPSTREAM Ugt86Di
2L	20321754	2L_20321754_SNP [dm3] 2L_20321754_SNP [dm6]	T	A	8.682e^-6	1	INTRON spir	TF binding site mE1_TFBS_cad
3R	24817233	3R_24817233_SNP [dm3] 3R_28991511_SNP [dm6]	G	C	1.012e^-5	1	INTERGENIC
3L	10193851	3L_10193851_SNP [dm3] 3L_10200751_SNP [dm6]	G	A	1.258e^-5	1	INTRON ect
3L	16502579	3L_16502579_SNP [dm3] 3L_16509479_SNP [dm6]	C	T	1.301e^-5	1	INTRON CG43373
2L	18792029	2L_18792029_SNP [dm3] 2L_18792029_SNP [dm6]	A	G	1.330e^-5	1	INTRON ham
2R	18610658	2R_18610658_DEL [dm3] 2R_22723153_DEL [dm6]	AA	A	1.372e^-5	1	INTRON jbug
3L	13984970	3L_13984970_SNP [dm3] 3L_13991870_SNP [dm6]	A	C	1.405e^-5	1	INTRON CG17364	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	19257371	3L_19257371_SNP [dm3] 3L_19264271_SNP [dm6]	T	A	1.482e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	1080805	3L_1080805_SNP [dm3] 3L_1080805_SNP [dm6]	G	A	1.573e^-5	1	INTRON bab1
2L	16395601	2L_16395601_SNP [dm3] 2L_16395601_SNP [dm6]	G	A	1.703e^-5	1	INTERGENIC
3R	22249607	3R_22249607_SNP [dm3] 3R_26423885_SNP [dm6]	G	A	1.746e^-5	1	DOWNSTREAM CG6503 INTERGENIC
3L	19256666	3L_19256666_SNP [dm3] 3L_19263566_SNP [dm6]	G	T	1.790e^-5	1	UPSTREAM CG9666 & 1 other INTRON Max	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	6798532	X_6798532_SNP [dm3] X_6904499_SNP [dm6]	C	T	1.808e^-5	1	INTERGENIC
3L	2524069	3L_2524069_SNP [dm3] 3L_2524069_SNP [dm6]	T	C	2.243e^-5	1	INTRON Spn	TF binding site mE1_TFBS_inv
3L	10330003	3L_10330003_DEL [dm3] 3L_10336903_DEL [dm6]	AAAGGCGGCCA...	A	2.269e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad
3R	3597690	3R_3597690_SNP [dm3] 3R_7771968_SNP [dm6]	G	A	2.299e^-5	1	UPSTREAM CG11286 INTERGENIC
2R	9606159	2R_9606159_SNP [dm3] 2R_13718654_SNP [dm6]	A	C	2.387e^-5	1	INTRON fas	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	19256489	3L_19256489_SNP [dm3] 3L_19263389_SNP [dm6]	T	A	2.472e^-5	1	UPSTREAM CG9666 & 1 other DOWNSTREAM Bet1 INTRON Max	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18151233	2R_18151233_SNP [dm3] 2R_22263728_SNP [dm6]	T	A	2.486e^-5	1	INTRON dve
2L	1065050	2L_1065050_SNP [dm3] 2L_1065050_SNP [dm6]	T	A	2.506e^-5	1	INTRON S	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	19257309	3L_19257309_SNP [dm3] 3L_19264209_SNP [dm6]	A	C	2.582e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	19257317	3L_19257317_SNP [dm3] 3L_19264217_SNP [dm6]	G	A	2.582e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	19764831	2L_19764831_SNP [dm3] 2L_19764831_SNP [dm6]	A	G	2.656e^-5	1	UPSTREAM fbp DOWNSTREAM bsh INTERGENIC	TF binding site mE1_TFBS_Trl
3R	16941940	3R_16941940_SNP [dm3] 3R_21116218_SNP [dm6]	T	A	2.724e^-5	1	UPSTREAM ppan DOWNSTREAM Rab11 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13012590	3L_13012590_SNP [dm3] 3L_13019490_SNP [dm6]	G	A	2.744e^-5	1	UTR_3_PRIME ste14 UPSTREAM CR45445 DOWNSTREAM AdenoK
2R	9606240	2R_9606240_SNP [dm3] 2R_13718735_SNP [dm6]	A	T	2.787e^-5	1	INTRON fas	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	19258961	3L_19258961_SNP [dm3] 3L_19265861_SNP [dm6]	T	C	2.796e^-5	1	UPSTREAM CG45081 DOWNSTREAM CG9629 INTRON CG9666 & 1 other
3L	3559398	3L_3559398_INS [dm3] 3L_3559398_INS [dm6]	CA	GCTG	2.823e^-5	1	INTRON Eip63E
3L	19257343	3L_19257343_SNP [dm3] 3L_19264243_SNP [dm6]	T	C	2.863e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	18526965	2L_18526965_SNP [dm3] 2L_18526965_SNP [dm6]	T	C	2.949e^-5	1	SYNONYMOUS_CODING CG10211	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	17818348	2L_17818348_SNP [dm3] 2L_17818348_SNP [dm6]	A	T	2.994e^-5	1	INTRON CadN2
3L	19256313	3L_19256313_SNP [dm3] 3L_19263213_SNP [dm6]	A	T	3.157e^-5	1	SPLICE_SITE_REGION Max UPSTREAM CG9666 & 1 other DOWNSTREAM Bet1 INTRON Max	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	24817741	3R_24817741_SNP [dm3] 3R_28992019_SNP [dm6]	C	G	3.209e^-5	1	DOWNSTREAM wat INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	17768323	2L_17768323_SNP [dm3] 2L_17768323_SNP [dm6]	G	A	3.224e^-5	1	INTRON CadN
3L	19256323	3L_19256323_SNP [dm3] 3L_19263223_SNP [dm6]	T	A	3.227e^-5	1	UPSTREAM CG9666 & 1 other DOWNSTREAM Bet1 INTRON Max	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	9219196	3L_9219196_DEL [dm3] 3L_9226096_DEL [dm6]	ACATTCCAGCTGTAAA...	A	3.241e^-5	1	INTERGENIC
2R	8174583	2R_8174583_SNP [dm3] 2R_12287078_SNP [dm6]	T	C	3.272e^-5	1	INTRON CG42700
3R	22420618	3R_22420618_SNP [dm3] 3R_26594896_SNP [dm6]	C	T	3.354e^-5	1	UTR_3_PRIME scrib INTRON scrib
3R	25832398	3R_25832398_SNP [dm3] 3R_30006676_SNP [dm6]	G	A	3.641e^-5	1	SYNONYMOUS_CODING CG7912 INTRON Nlp
3R	23130932	3R_23130932_SNP [dm3] 3R_27305210_SNP [dm6]	G	C	3.669e^-5	1	INTRON CG3339	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	3297190	X_3297190_SNP [dm3] X_3403157_SNP [dm6]	C	T	3.772e^-5	1	INTRON CR44999 & 1 other
2L	14511668	2L_14511668_SNP [dm3] 2L_14511668_SNP [dm6]	C	T	3.786e^-5	1	EXON CR45693	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	19257473	3L_19257473_SNP [dm3] 3L_19264373_SNP [dm6]	A	T	3.829e^-5	1	UTR_5_PRIME CG42374 & 1 other UPSTREAM CG9666 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	19257398	3L_19257398_SNP [dm3] 3L_19264298_SNP [dm6]	T	A	3.838e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	17541683	2L_17541683_SNP [dm3] 2L_17541683_SNP [dm6]	C	T	3.881e^-5	1	UPSTREAM CR43304 INTERGENIC
2R	13795784	2R_13795784_SNP [dm3] 2R_17908279_SNP [dm6]	C	T	3.936e^-5	1	INTRON Elk
3L	17663573	3L_17663573_SNP [dm3] 3L_17670473_SNP [dm6]	A	T	4.046e^-5	1	INTERGENIC
2R	18151188	2R_18151188_SNP [dm3] 2R_22263683_SNP [dm6]	T	C	4.108e^-5	1	INTRON dve
3R	25840277	3R_25840277_SNP [dm3] 3R_30014555_SNP [dm6]	A	G	4.136e^-5	1	DOWNSTREAM Mgat2 INTRON CG7920	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3L	19261595	3L_19261595_DEL [dm3] 3L_19268495_DEL [dm6]	TAAATTTGTTATCA...	T	4.150e^-5	1	UPSTREAM CG14085 INTRON CG9629	TF binding site mE1_TFBS_cad
2R	9606221	2R_9606221_DEL [dm3] 2R_13718716_DEL [dm6]	TGCGCTTGT	T	4.167e^-5	1	INTRON fas	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	18399894	2R_18399894_SNP [dm3] 2R_22512389_SNP [dm6]	T	C	4.169e^-5	1	INTRON px	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_Ubx
3R	25830251	3R_25830251_SNP [dm3] 3R_30004529_SNP [dm6]	C	T	4.304e^-5	1	UPSTREAM Nlp DOWNSTREAM Tace INTRON CG7911	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	1050701	2L_1050701_SNP [dm3] 2L_1050701_SNP [dm6]	C	T	4.354e^-5	1	UTR_3_PRIME S	TF binding site mE1_TFBS_HSA
3L	13988902	3L_13988902_DEL [dm3] 3L_13995802_DEL [dm6]	GTACTTA	G	4.363e^-5	1	INTRON 26-29-p	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	27473879	3R_27473879_SNP [dm3] 3R_31648157_SNP [dm6]	T	A	4.410e^-5	1	INTRON kek6
3L	17180432	3L_17180432_SNP [dm3] 3L_17187332_SNP [dm6]	G	T	4.440e^-5	1	INTRON Rbp6
3L	13988889	3L_13988889_SNP [dm3] 3L_13995789_SNP [dm6]	A	T	4.465e^-5	1	INTRON 26-29-p	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	19257336	3L_19257336_SNP [dm3] 3L_19264236_SNP [dm6]	A	C	4.672e^-5	1	UPSTREAM CG9666 & 2 others INTRON CG9666 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	7673484	2R_7673484_SNP [dm3] 2R_11785979_SNP [dm6]	A	C	4.695e^-5	1	INTRON ths
2L	17780307	2L_17780307_SNP [dm3] 2L_17780307_SNP [dm6]	C	A	4.711e^-5	1	INTERGENIC
2L	14573684	2L_14573684_SNP [dm3] 2L_14573684_SNP [dm6]	C	T	4.800e^-5	1	INTERGENIC
2R	14516091	2R_14516091_SNP [dm3] 2R_18628586_SNP [dm6]	C	T	4.805e^-5	1	SYNONYMOUS_CODING Eip55E DOWNSTREAM Sec6	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	12371079	2R_12371079_SNP [dm3] 2R_16483574_SNP [dm6]	A	G	4.829e^-5	1	INTERGENIC
2R	9606197	2R_9606197_SNP [dm3] 2R_13718692_SNP [dm6]	T	C	4.891e^-5	1	INTRON fas	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	17570972	2R_17570972_SNP [dm3] 2R_21683467_SNP [dm6]	G	A	4.942e^-5	1	NON_SYNONYMOUS_CODING CG30263	TF binding site mE1_TFBS_cad
2L	14427462	2L_14427462_SNP [dm3] 2L_14427462_SNP [dm6]	A	T	4.965e^-5	1	INTERGENIC
3L	13988892	3L_13988892_SNP [dm3] 3L_13995792_SNP [dm6]	C	T	5.176e^-5	1	INTRON 26-29-p	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	19257012	3L_19257012_SNP [dm3] 3L_19263912_SNP [dm6]	A	T	5.194e^-5	1	SPLICE_SITE_REGION Max START_GAINED CG9666 & 1 other UTR_5_PRIME CG9666 & 1 other UPSTREAM CG9666 & 1 other INTRON Max	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	19256478	3L_19256478_SNP [dm3] 3L_19263378_SNP [dm6]	A	G	5.249e^-5	1	UPSTREAM CG9666 & 1 other DOWNSTREAM Bet1 INTRON Max	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	684965	2L_684965_DEL [dm3] 2L_684965_DEL [dm6]	TTCCTT	T	5.268e^-5	1	INTRON ds	TF binding site BDTNP1_TFBS_dl
X	13956224	X_13956224_SNP [dm3] X_14062191_SNP [dm6]	C	T	5.302e^-5	1	UPSTREAM Ste:CG33236 INTERGENIC
2R	9606192	2R_9606192_SNP [dm3] 2R_13718687_SNP [dm6]	C	G	5.319e^-5	1	INTRON fas	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	19258436	3L_19258436_SNP [dm3] 3L_19265336_SNP [dm6]	T	C	5.345e^-5	1	SYNONYMOUS_CODING CG9666 UTR_3_PRIME CG42374 UPSTREAM CG45081	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	15146275	X_15146275_SNP [dm3] X_15252242_SNP [dm6]	A	G	5.348e^-5	1	INTERGENIC
2L	19947938	2L_19947938_SNP [dm3] 2L_19947938_SNP [dm6]	G	A	5.405e^-5	1	INTRON sick
2R	19519512	2R_19519512_SNP [dm3] 2R_23631989_SNP [dm6]	A	G	5.453e^-5	1	UPSTREAM retn INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl
2L	8797983	2L_8797983_SNP [dm3] 2L_8797983_SNP [dm6]	G	T	5.503e^-5	1	INTERGENIC
2R	5250893	2R_5250893_SNP [dm3] 2R_9363388_SNP [dm6]	T	C	5.536e^-5	1	UPSTREAM CG12158 INTRON CG13954
2R	3744188	2R_3744188_SNP [dm3] 2R_7856683_SNP [dm6]	A	T	5.648e^-5	1	INTRON Dgk
2L	20364442	2L_20364442_SNP [dm3] 2L_20364442_SNP [dm6]	C	T	5.720e^-5	1	SYNONYMOUS_CODING RtGEF UTR_3_PRIME RtGEF DOWNSTREAM RtGEF
2L	9301668	2L_9301668_SNP [dm3] 2L_9301668_SNP [dm6]	T	G	5.757e^-5	1	UTR_3_PRIME Ggamma30A
2L	19865680	2L_19865680_SNP [dm3] 2L_19865680_SNP [dm6]	T	C	5.882e^-5	1	UPSTREAM sick INTRON sick	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3R	6983761	3R_6983761_SNP [dm3] 3R_11158039_SNP [dm6]	A	T	6.008e^-5	1	INTRON Ugt86Da
2L	18537420	2L_18537420_SNP [dm3] 2L_18537420_SNP [dm6]	A	G	6.086e^-5	1	SYNONYMOUS_CODING Pde11	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	17768131	2L_17768131_SNP [dm3] 2L_17768131_SNP [dm6]	C	T	6.128e^-5	1	INTRON CadN
3L	17664843	3L_17664843_SNP [dm3] 3L_17671743_SNP [dm6]	A	C	6.138e^-5	1	UPSTREAM CG34251 INTRON CG34251
2L	18486593	2L_18486593_SNP [dm3] 2L_18486593_SNP [dm6]	G	A	6.283e^-5	1	INTRON CG10176	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_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	843790	3L_843790_SNP [dm3] 3L_843790_SNP [dm6]	G	A	6.296e^-5	1	UPSTREAM CG13889 DOWNSTREAM Gr61a INTERGENIC
X	6798572	X_6798572_SNP [dm3] X_6904539_SNP [dm6]	T	A	6.300e^-5	1	INTERGENIC

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By genomic position
Variant impact
Gene name

PC5_Nutri_Score_High phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results