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=1.131e^-4)
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	0.08626

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1453 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	1109009	2L_1109009_SNP [dm3] 2L_1109009_SNP [dm6]	T	C	9.169e^-6	0.414	SYNONYMOUS_CODING CG14339 UPSTREAM mtRNApol	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Ubx
2R	4685258	2R_4685258_SNP [dm3] 2R_8797753_SNP [dm6]	C	G	9.169e^-6	0.414	UPSTREAM sns INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl
2L	1114134	2L_1114134_SNP [dm3] 2L_1114134_SNP [dm6]	T	A	1.412e^-5	0.414	UTR_3_PRIME CG14340 DOWNSTREAM Pino
2L	16765997	2L_16765997_SNP [dm3] 2L_16765997_SNP [dm6]	T	C	1.412e^-5	0.414	UPSTREAM Mhc INTERGENIC
2L	19368143	2L_19368143_SNP [dm3] 2L_19368143_SNP [dm6]	A	T	2.035e^-5	0.414	INTERGENIC
2L	10125642	2L_10125642_SNP [dm3] 2L_10125642_SNP [dm6]	A	T	3.453e^-5	0.414	UTR_3_PRIME CG34109 INTRON CG44153
2L	1105107	2L_1105107_DEL [dm3] 2L_1105107_DEL [dm6]	AA	A	3.453e^-5	0.414	SPLICE_SITE_REGION mtRNApol INTRON mtRNApol	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1105125	2L_1105125_SNP [dm3] 2L_1105125_SNP [dm6]	G	A	3.453e^-5	0.414	INTRON mtRNApol	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1105243	2L_1105243_SNP [dm3] 2L_1105243_SNP [dm6]	C	G	3.453e^-5	0.414	SYNONYMOUS_CODING mtRNApol	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1109393	2L_1109393_SNP [dm3] 2L_1109393_SNP [dm6]	G	A	3.453e^-5	0.414	SYNONYMOUS_CODING CG14339	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv mE1_TFBS_sens
2L	1109513	2L_1109513_SNP [dm3] 2L_1109513_SNP [dm6]	C	T	3.453e^-5	0.414	SYNONYMOUS_CODING CG14339	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
2L	1111513	2L_1111513_SNP [dm3] 2L_1111513_SNP [dm6]	C	A	3.453e^-5	0.414	NON_SYNONYMOUS_CODING CG14339
2L	1111676	2L_1111676_SNP [dm3] 2L_1111676_SNP [dm6]	C	T	3.453e^-5	0.414	SYNONYMOUS_CODING CG14339	TF binding site mE1_TFBS_chinmo
2L	16594262	2L_16594262_SNP [dm3] 2L_16594262_SNP [dm6]	C	A	3.453e^-5	0.414	INTRON CG42389
2L	16594263	2L_16594263_SNP [dm3] 2L_16594263_SNP [dm6]	C	T	3.453e^-5	0.414	INTRON CG42389
2L	16802183	2L_16802183_SNP [dm3] 2L_16802183_SNP [dm6]	A	C	3.453e^-5	0.414	NON_SYNONYMOUS_CODING CG13280 DOWNSTREAM Ugt36Bc
2L	17634712	2L_17634712_SNP [dm3] 2L_17634712_SNP [dm6]	G	A	3.453e^-5	0.414	INTERGENIC
2L	17636139	2L_17636139_SNP [dm3] 2L_17636139_SNP [dm6]	T	A	3.453e^-5	0.414	INTERGENIC
2L	17636141	2L_17636141_SNP [dm3] 2L_17636141_SNP [dm6]	A	G	3.453e^-5	0.414	INTERGENIC
2L	17636143	2L_17636143_SNP [dm3] 2L_17636143_SNP [dm6]	A	T	3.453e^-5	0.414	INTERGENIC
2L	17636160	2L_17636160_DEL [dm3] 2L_17636160_DEL [dm6]	GG	A	3.453e^-5	0.414	INTERGENIC
2L	20377635	2L_20377635_SNP [dm3] 2L_20377635_SNP [dm6]	T	G	3.453e^-5	0.414	INTRON CG16798
2L	20379440	2L_20379440_SNP [dm3] 2L_20379440_SNP [dm6]	C	T	3.453e^-5	0.414	NON_SYNONYMOUS_CODING CG16798
X	10505725	X_10505725_SNP [dm3] X_10611692_SNP [dm6]	A	G	4.223e^-5	0.414	SYNONYMOUS_CODING CG43347	TF binding site BDTNP1_TFBS_ftz mE1_TFBS_chinmo
2R	15294833	2R_15294833_SNP [dm3] 2R_19407328_SNP [dm6]	A	G	4.692e^-5	0.414	INTRON hts
2L	14803636	2L_14803636_SNP [dm3] 2L_14803636_SNP [dm6]	T	C	5.020e^-5	0.414	DOWNSTREAM CG33308 INTERGENIC
2L	4318113	2L_4318113_SNP [dm3] 2L_4318113_SNP [dm6]	T	C	5.020e^-5	0.414	INTRON tutl	TF binding site mE1_TFBS_HSA
2L	5930749	2L_5930749_SNP [dm3] 2L_5930749_SNP [dm6]	G	T	5.047e^-5	0.414	INTRON dsf
2R	14781302	2R_14781302_SNP [dm3] 2R_18893797_SNP [dm6]	A	C	5.203e^-5	0.414	INTRON sano
2L	674784	2L_674784_SNP [dm3] 2L_674784_SNP [dm6]	T	A	5.327e^-5	0.414	INTRON ds
2R	12385453	2R_12385453_SNP [dm3] 2R_16497948_SNP [dm6]	C	G	5.327e^-5	0.414	NON_SYNONYMOUS_CODING CG7813
2R	13671870	2R_13671870_SNP [dm3] 2R_17784365_SNP [dm6]	C	T	5.327e^-5	0.414	UPSTREAM mir-31a INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	7528403	2R_7528403_SNP [dm3] 2R_11640898_SNP [dm6]	C	G	5.327e^-5	0.414	UTR_5_PRIME CG9005 DOWNSTREAM CG9003	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2R	7540681	2R_7540681_SNP [dm3] 2R_11653176_SNP [dm6]	C	T	5.327e^-5	0.414	UPSTREAM tRNA:CR30254 DOWNSTREAM CG34228 & 1 other INTRON Roc2	TF binding site mE1_TFBS_cad
X	15285687	X_15285687_SNP [dm3] X_15391654_SNP [dm6]	G	T	5.327e^-5	0.414	INTRON Cngl
X	15286206	X_15286206_SNP [dm3] X_15392173_SNP [dm6]	C	T	5.327e^-5	0.414	INTRON Cngl
2R	14522723	2R_14522723_SNP [dm3] 2R_18635218_SNP [dm6]	C	A	5.520e^-5	0.414	INTRON CG30122	TF binding site BDTNP1_TFBS_dl
2L	14324624	2L_14324624_SNP [dm3] 2L_14324624_SNP [dm6]	G	A	5.608e^-5	0.414	SYNONYMOUS_CODING wb	TF binding site mE1_TFBS_cad
2L	6229430	2L_6229430_SNP [dm3] 2L_6229430_SNP [dm6]	C	T	5.608e^-5	0.414	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
2L	8718964	2L_8718964_SNP [dm3] 2L_8718964_SNP [dm6]	G	C	5.608e^-5	0.414	INTRON raw	TF binding site mE1_TFBS_Trl
3L	11450024	3L_11450024_SNP [dm3] 3L_11456924_SNP [dm6]	T	A	5.956e^-5	0.414	DOWNSTREAM CG12289 INTERGENIC
2R	13827752	2R_13827752_SNP [dm3] 2R_17940247_SNP [dm6]	T	C	5.979e^-5	0.414	INTERGENIC
2R	13829228	2R_13829228_SNP [dm3] 2R_17941723_SNP [dm6]	G	C	5.979e^-5	0.414	INTERGENIC
3R	13709627	3R_13709627_SNP [dm3] 3R_17883905_SNP [dm6]	C	G	5.979e^-5	0.414	SYNONYMOUS_CODING Rim INTRON Rim	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	16655897	X_16655897_INS [dm3] X_16761864_INS [dm6]	C	CAGGCC	5.979e^-5	0.414	INTRON if
2L	1111222	2L_1111222_SNP [dm3] 2L_1111222_SNP [dm6]	C	T	6.010e^-5	0.414	INTRON CG14339
2L	10413683	2L_10413683_SNP [dm3] 2L_10413683_SNP [dm6]	T	G	6.149e^-5	0.414	UPSTREAM Klp31E & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
X	13675629	X_13675629_SNP [dm3] X_13781596_SNP [dm6]	T	C	6.149e^-5	0.414	SYNONYMOUS_CODING CtsB1 UPSTREAM CG11103	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr
2L	1113327	2L_1113327_SNP [dm3] 2L_1113327_SNP [dm6]	G	A	6.352e^-5	0.414	NON_SYNONYMOUS_CODING CG14340 DOWNSTREAM CG14339
2L	1113552	2L_1113552_SNP [dm3] 2L_1113552_SNP [dm6]	C	T	6.352e^-5	0.414	SPLICE_SITE_REGION CG14340 DOWNSTREAM CG14339 INTRON CG14340
2L	1114376	2L_1114376_SNP [dm3] 2L_1114376_SNP [dm6]	A	T	6.352e^-5	0.414	DOWNSTREAM Pino & 1 other INTERGENIC
2L	1114514	2L_1114514_SNP [dm3] 2L_1114514_SNP [dm6]	G	T	6.352e^-5	0.414	DOWNSTREAM Pino & 1 other INTERGENIC
2L	1116164	2L_1116164_SNP [dm3] 2L_1116164_SNP [dm6]	C	T	6.352e^-5	0.414	INTRON Pino	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	1116297	2L_1116297_SNP [dm3] 2L_1116297_SNP [dm6]	A	G	6.352e^-5	0.414	INTRON Pino	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	12696136	2L_12696136_SNP [dm3] 2L_12696136_SNP [dm6]	A	T	6.352e^-5	0.414	SPLICE_SITE_REGION PICK1 START_GAINED PICK1 UTR_5_PRIME PICK1 UPSTREAM PICK1 DOWNSTREAM CG5781 INTRON PICK1
2L	16765887	2L_16765887_SNP [dm3] 2L_16765887_SNP [dm6]	T	C	6.352e^-5	0.414	UPSTREAM Mhc INTERGENIC
2R	14623931	2R_14623931_SNP [dm3] 2R_18736426_SNP [dm6]	T	G	6.352e^-5	0.414	INTRON Hs3st-A
3R	19564473	3R_19564473_SNP [dm3] 3R_23738751_SNP [dm6]	A	G	6.480e^-5	0.414	INTRON Hmgcr
3R	19564500	3R_19564500_SNP [dm3] 3R_23738778_SNP [dm6]	A	G	6.480e^-5	0.414	INTRON Hmgcr
3R	19794096	3R_19794096_SNP [dm3] 3R_23968374_SNP [dm6]	A	G	6.480e^-5	0.414	INTRON CG31140
2L	21757684	2L_21757684_SNP [dm3] 2L_21757684_SNP [dm6]	A	T	6.627e^-5	0.414	UPSTREAM CG1416 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
2L	17636231	2L_17636231_SNP [dm3] 2L_17636231_SNP [dm6]	G	T	7.120e^-5	0.414	INTERGENIC
3L	9164489	3L_9164489_SNP [dm3] 3L_9171389_SNP [dm6]	A	C	7.222e^-5	0.414	INTRON Rdl
2L	8720250	2L_8720250_SNP [dm3] 2L_8720250_SNP [dm6]	A	C	7.564e^-5	0.414	INTRON raw
2L	8978435	2L_8978435_SNP [dm3] 2L_8978435_SNP [dm6]	G	A	7.570e^-5	0.414	SYNONYMOUS_CODING CG13101
X	22330570	X_22330570_SNP [dm3] X_22928734_SNP [dm6]	C	A	7.778e^-5	0.414	INTERGENIC
X	22333095	X_22333095_SNP [dm3] X_22931259_SNP [dm6]	A	T	7.778e^-5	0.414	INTERGENIC	transposable element FlyBase
2L	15080821	2L_15080821_SNP [dm3] 2L_15080821_SNP [dm6]	A	G	7.804e^-5	0.414	INTRON CG15270
2L	15115080	2L_15115080_SNP [dm3] 2L_15115080_SNP [dm6]	G	A	7.804e^-5	0.414	NON_SYNONYMOUS_CODING stc	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3226988	2L_3226988_SNP [dm3] 2L_3226988_SNP [dm6]	A	T	7.934e^-5	0.414	INTERGENIC
2R	13575617	2R_13575617_SNP [dm3] 2R_17688112_SNP [dm6]	C	T	7.934e^-5	0.414	SYNONYMOUS_CODING HPS4	TF binding site mE1_TFBS_sens
2R	14781232	2R_14781232_SNP [dm3] 2R_18893727_SNP [dm6]	G	T	7.934e^-5	0.414	INTRON sano
2R	14781336	2R_14781336_SNP [dm3] 2R_18893831_SNP [dm6]	A	T	7.934e^-5	0.414	INTRON sano
2R	16996791	2R_16996791_SNP [dm3] 2R_21109286_SNP [dm6]	G	A	7.934e^-5	0.414	INTRON ktub
3R	11443019	3R_11443019_SNP [dm3] 3R_15617297_SNP [dm6]	C	T	7.934e^-5	0.414	INTERGENIC
3R	11443027	3R_11443027_SNP [dm3] 3R_15617305_SNP [dm6]	C	A	7.934e^-5	0.414	INTERGENIC
3L	14865936	3L_14865936_SNP [dm3] 3L_14872836_SNP [dm6]	T	A	7.984e^-5	0.414	INTRON CG17839	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14865939	3L_14865939_SNP [dm3] 3L_14872839_SNP [dm6]	T	G	7.984e^-5	0.414	INTRON CG17839	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14865951	3L_14865951_SNP [dm3] 3L_14872851_SNP [dm6]	T	G	7.984e^-5	0.414	INTRON CG17839	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14866016	3L_14866016_SNP [dm3] 3L_14872916_SNP [dm6]	T	A	7.984e^-5	0.414	INTRON CG17839	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	3111268	3L_3111268_SNP [dm3] 3L_3111268_SNP [dm6]	G	T	7.984e^-5	0.414	UPSTREAM CG45066 DOWNSTREAM CG45067 INTERGENIC
2L	10129394	2L_10129394_SNP [dm3] 2L_10129394_SNP [dm6]	G	C	8.096e^-5	0.414	INTRON CG44153	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	10129396	2L_10129396_SNP [dm3] 2L_10129396_SNP [dm6]	T	A	8.096e^-5	0.414	INTRON CG44153	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	16994360	2R_16994360_SNP [dm3] 2R_21106855_SNP [dm6]	C	T	8.096e^-5	0.414	INTRON ktub	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	5521255	3L_5521255_SNP [dm3] 3L_5528155_SNP [dm6]	T	A	8.096e^-5	0.414	INTRON Lkr
3L	5521324	3L_5521324_SNP [dm3] 3L_5528224_SNP [dm6]	G	T	8.096e^-5	0.414	INTRON Lkr
3L	9875936	3L_9875936_SNP [dm3] 3L_9882836_SNP [dm6]	G	A	8.096e^-5	0.414	SYNONYMOUS_CODING CG34382	TF binding site mE1_TFBS_chinmo
X	5442980	X_5442980_SNP [dm3] X_5548947_SNP [dm6]	T	G	8.096e^-5	0.414	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11416012	2L_11416012_SNP [dm3] 2L_11416012_SNP [dm6]	T	C	8.234e^-5	0.414	INTERGENIC
X	18861119	X_18861119_SNP [dm3] X_18967086_SNP [dm6]	G	C	8.266e^-5	0.414	INTRON CG43759	TF binding site mE1_TFBS_inv
X	13675626	X_13675626_SNP [dm3] X_13781593_SNP [dm6]	A	G	8.517e^-5	0.414	SYNONYMOUS_CODING CtsB1 UPSTREAM CG11103	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr
2L	4253907	2L_4253907_SNP [dm3] 2L_4253907_SNP [dm6]	A	C	8.903e^-5	0.414	INTERGENIC
2R	14091123	2R_14091123_SNP [dm3] 2R_18203618_SNP [dm6]	A	G	8.903e^-5	0.414	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16049248	2R_16049248_SNP [dm3] 2R_20161743_SNP [dm6]	A	G	8.903e^-5	0.414	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16994815	2R_16994815_SNP [dm3] 2R_21107310_SNP [dm6]	C	A	8.903e^-5	0.414	INTRON ktub
2R	5263484	2R_5263484_SNP [dm3] 2R_9375979_SNP [dm6]	A	G	8.903e^-5	0.414	INTRON CG13954
2R	5264469	2R_5264469_SNP [dm3] 2R_9376964_SNP [dm6]	A	G	8.903e^-5	0.414	INTRON CG13954	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	5265008	2R_5265008_SNP [dm3] 2R_9377503_SNP [dm6]	A	G	8.903e^-5	0.414	INTRON CG13954
2R	5265058	2R_5265058_SNP [dm3] 2R_9377553_SNP [dm6]	C	A	8.903e^-5	0.414	INTRON CG13954
2R	7950569	2R_7950569_SNP [dm3] 2R_12063064_SNP [dm6]	A	T	8.903e^-5	0.414	DOWNSTREAM Drep-3 INTERGENIC

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By genomic position
Variant impact
Gene name

Makeham phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results