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=3.919e^-5)
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	0.07133

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.806	0.0333

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1988 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	10784964	3L_10784964_SNP [dm3] 3L_10791864_SNP [dm6]	C	T	1.664e^-6	0.91	INTERGENIC
2L	17394794	2L_17394794_DEL [dm3] 2L_17394794_DEL [dm6]	ACACGTGA	A	2.971e^-6	0.91	INTRON CLIP-190
X	8184377	X_8184377_SNP [dm3] X_8290344_SNP [dm6]	C	T	4.258e^-6	0.91	INTRON nAChRalpha3
2R	10133755	2R_10133755_SNP [dm3] 2R_14246250_SNP [dm6]	C	A	4.446e^-6	0.91	UPSTREAM Mdr50 DOWNSTREAM CG8503 INTERGENIC
2L	17394834	2L_17394834_INS [dm3] 2L_17394834_INS [dm6]	G	GCATAGGTACTTTAGTTATA...	5.729e^-6	0.91	INTRON CLIP-190
2L	1948749	2L_1948749_SNP [dm3] 2L_1948749_SNP [dm6]	A	G	5.775e^-6	0.91	INTERGENIC	regulatory region REDfly_CRMs
3R	27476678	3R_27476678_SNP [dm3] 3R_31650956_SNP [dm6]	T	C	6.161e^-6	0.91	INTRON kek6
3L	4947200	3L_4947200_SNP [dm3] 3L_4947200_SNP [dm6]	A	T	6.289e^-6	0.91	INTRON Con
3R	8364009	3R_8364009_SNP [dm3] 3R_12538287_SNP [dm6]	T	G	7.117e^-6	0.91	INTRON Octbeta3R
3L	18564371	3L_18564371_SNP [dm3] 3L_18571271_SNP [dm6]	C	T	7.609e^-6	0.91	INTRON AstC-R1
2L	19590589	2L_19590589_SNP [dm3] 2L_19590589_SNP [dm6]	T	G	8.023e^-6	0.91	INTRON Lar	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA
3R	26321298	3R_26321298_SNP [dm3] 3R_30495576_SNP [dm6]	G	A	8.343e^-6	0.91	INTRON PH4alphaMP	TF binding site mE1_TFBS_inv
2L	12762833	2L_12762833_SNP [dm3] 2L_12762833_SNP [dm6]	C	T	1.002e^-5	0.91	UPSTREAM CG15483 INTERGENIC
2R	10214427	2R_10214427_SNP [dm3] 2R_14326922_SNP [dm6]	T	C	1.040e^-5	0.91	SYNONYMOUS_CODING Shroom	TF binding site mE1_TFBS_cad
2R	10214815	2R_10214815_SNP [dm3] 2R_14327310_SNP [dm6]	A	G	1.149e^-5	0.91	INTRON Shroom	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	17176694	X_17176694_SNP [dm3] X_17282661_SNP [dm6]	C	A	1.160e^-5	0.91	SYNONYMOUS_CODING CG8664 UTR_5_PRIME CG5445	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
3R	10349795	3R_10349795_SNP [dm3] 3R_14524073_SNP [dm6]	C	T	1.172e^-5	0.91	INTRON Pde6
2L	2473735	2L_2473735_SNP [dm3] 2L_2473735_SNP [dm6]	A	T	1.206e^-5	0.91	UPSTREAM CR45286 INTERGENIC	regulatory region REDfly_CRMs
3L	4937828	3L_4937828_SNP [dm3] 3L_4937828_SNP [dm6]	C	T	1.318e^-5	0.91	UTR_3_PRIME Con DOWNSTREAM Con
X	6530203	X_6530203_SNP [dm3] X_6636170_SNP [dm6]	G	A	1.344e^-5	0.91	UPSTREAM CR44817 DOWNSTREAM CG14443 INTRON pigs
3R	14672743	3R_14672743_SNP [dm3] 3R_18847021_SNP [dm6]	T	A	1.441e^-5	0.91	INTRON CG18208
3R	9909155	3R_9909155_SNP [dm3] 3R_14083433_SNP [dm6]	C	A	1.443e^-5	0.91	INTRON foxo
2R	2855654	2R_2855654_SNP [dm3] 2R_6968149_SNP [dm6]	G	C	1.586e^-5	0.91	INTRON mim & 1 other
X	8184385	X_8184385_SNP [dm3] X_8290352_SNP [dm6]	G	T	1.609e^-5	0.91	INTRON nAChRalpha3
2R	10134908	2R_10134908_SNP [dm3] 2R_14247403_SNP [dm6]	A	G	1.632e^-5	0.91	INTRON Mdr50
2R	11809104	2R_11809104_SNP [dm3] 2R_15921599_SNP [dm6]	T	A	1.667e^-5	0.91	INTRON sli	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	11735503	2R_11735503_SNP [dm3] 2R_15847998_SNP [dm6]	C	G	1.882e^-5	0.91	UPSTREAM CG8249 & 1 other INTRON tun	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_bab1 mE1_TFBS_HSA
2R	10133855	2R_10133855_SNP [dm3] 2R_14246350_SNP [dm6]	A	T	1.968e^-5	0.91	UPSTREAM Mdr50 DOWNSTREAM CG8503 INTERGENIC
2R	10135658	2R_10135658_SNP [dm3] 2R_14248153_SNP [dm6]	C	T	2.062e^-5	0.91	SYNONYMOUS_CODING Mdr50
2R	10021882	2R_10021882_SNP [dm3] 2R_14134377_SNP [dm6]	G	T	2.088e^-5	0.91	INTRON Prosap
2R	10136712	2R_10136712_SNP [dm3] 2R_14249207_SNP [dm6]	C	T	2.130e^-5	0.91	NON_SYNONYMOUS_CODING Mdr50	TF binding site mE1_TFBS_cad
3L	9622447	3L_9622447_SNP [dm3] 3L_9629347_SNP [dm6]	A	G	2.162e^-5	0.91	UPSTREAM CG8336 & 1 other INTRON CG8336
2L	18909085	2L_18909085_SNP [dm3] 2L_18909085_SNP [dm6]	T	C	2.270e^-5	0.91	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2L	18909112	2L_18909112_SNP [dm3] 2L_18909112_SNP [dm6]	T	C	2.385e^-5	0.91	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	10135360	2R_10135360_SNP [dm3] 2R_14247855_SNP [dm6]	C	T	2.414e^-5	0.91	INTRON Mdr50
2R	10021914	2R_10021914_INS [dm3] 2R_14134409_INS [dm6]	TC	AAGT	2.467e^-5	0.91	INTRON Prosap
2L	10648575	2L_10648575_SNP [dm3] 2L_10648575_SNP [dm6]	C	A	2.504e^-5	0.91	NON_SYNONYMOUS_CODING CG17097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_run mE1_TFBS_sens
2L	15431279	2L_15431279_SNP [dm3] 2L_15431279_SNP [dm6]	T	C	2.639e^-5	0.91	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	10345795	3R_10345795_SNP [dm3] 3R_14520073_SNP [dm6]	G	T	2.677e^-5	0.91	UPSTREAM Cyp313a1 INTRON Pde6
X	21905879	X_21905879_SNP [dm3] X_22504043_SNP [dm6]	T	C	2.789e^-5	0.91	DOWNSTREAM l_1_G0196 INTRON l_1_G0196
2R	10135408	2R_10135408_SNP [dm3] 2R_14247903_SNP [dm6]	G	A	2.910e^-5	0.91	INTRON Mdr50
3R	10352413	3R_10352413_SNP [dm3] 3R_14526691_SNP [dm6]	T	C	2.955e^-5	0.91	INTRON Pde6
3R	8363784	3R_8363784_DEL [dm3] 3R_12538062_DEL [dm6]	AGGGGTTTAACTA...	A	3.035e^-5	0.91	INTRON Octbeta3R
3R	6876905	3R_6876905_SNP [dm3] 3R_11051183_SNP [dm6]	G	T	3.236e^-5	0.91	INTERGENIC
3R	23670674	3R_23670674_SNP [dm3] 3R_27844952_SNP [dm6]	T	A	3.275e^-5	0.91	UPSTREAM Or98P & 1 other INTRON CG34353
2R	10135272	2R_10135272_SNP [dm3] 2R_14247767_SNP [dm6]	A	C	3.283e^-5	0.91	INTRON Mdr50
2L	19737165	2L_19737165_SNP [dm3] 2L_19737165_SNP [dm6]	A	G	3.380e^-5	0.91	DOWNSTREAM Nf-YB INTERGENIC
3R	27476284	3R_27476284_SNP [dm3] 3R_31650562_SNP [dm6]	C	T	3.399e^-5	0.91	INTRON kek6
2L	21918567	2L_21918567_SNP [dm3] 2L_21918567_SNP [dm6]	C	T	3.482e^-5	0.91	INTRON CG11634
3L	3183841	3L_3183841_SNP [dm3] 3L_3183841_SNP [dm6]	A	G	3.487e^-5	0.91	UPSTREAM CG42494 INTRON Girdin
3L	7845930	3L_7845930_SNP [dm3] 3L_7852830_SNP [dm6]	A	G	3.519e^-5	0.91	INTRON Pdp1
3R	10370747	3R_10370747_SNP [dm3] 3R_14545025_SNP [dm6]	C	A	3.554e^-5	0.91	INTRON Pde6
2L	17394936	2L_17394936_SNP [dm3] 2L_17394936_SNP [dm6]	T	A	3.555e^-5	0.91	INTRON CLIP-190
2L	3220607	2L_3220607_DEL [dm3] 2L_3220607_DEL [dm6]	AATCACAAT	A	3.563e^-5	0.91	INTERGENIC
2R	6509019	2R_6509019_SNP [dm3] 2R_10621514_SNP [dm6]	T	G	3.711e^-5	0.91	UPSTREAM CG11883 INTRON CG11883
3R	6279172	3R_6279172_DEL [dm3] 3R_10453450_DEL [dm6]	ATTTAAA	A	3.724e^-5	0.91	INTERGENIC
2L	11951357	2L_11951357_SNP [dm3] 2L_11951357_SNP [dm6]	G	A	3.746e^-5	0.91	DOWNSTREAM CR43314 INTERGENIC
2L	2505579	2L_2505579_SNP [dm3] 2L_2505579_SNP [dm6]	T	G	3.789e^-5	0.91	INTERGENIC
X	17176035	X_17176035_SNP [dm3] X_17282002_SNP [dm6]	A	C	3.829e^-5	0.91	NON_SYNONYMOUS_CODING CG8664 UPSTREAM CG5445	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	13835322	3L_13835322_SNP [dm3] 3L_13842222_SNP [dm6]	A	G	3.981e^-5	0.91	UTR_5_PRIME CG8757 DOWNSTREAM CG8750	TF binding site mE1_TFBS_cad
2L	19587673	2L_19587673_DEL [dm3] 2L_19587673_DEL [dm6]	TGTT	T	3.981e^-5	0.91	INTRON Lar	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	15124385	2L_15124385_INS [dm3] 2L_15124385_INS [dm6]	A	AAGCTATAATA...	4.006e^-5	0.91	INTERGENIC
2L	11951342	2L_11951342_SNP [dm3] 2L_11951342_SNP [dm6]	A	C	4.043e^-5	0.91	DOWNSTREAM CR43314 INTERGENIC
2L	12638336	2L_12638336_SNP [dm3] 2L_12638336_SNP [dm6]	A	G	4.102e^-5	0.91	INTRON Ref2	TF binding site BDTNP1_TFBS_twi
2R	10135379	2R_10135379_SNP [dm3] 2R_14247874_SNP [dm6]	T	C	4.168e^-5	0.91	INTRON Mdr50
2R	11730628	2R_11730628_SNP [dm3] 2R_15843123_SNP [dm6]	G	T	4.178e^-5	0.91	UTR_3_PRIME CG8249 DOWNSTREAM CG8249 INTRON tun	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2L	17390180	2L_17390180_SNP [dm3] 2L_17390180_SNP [dm6]	G	C	4.294e^-5	0.91	INTRON CLIP-190
2L	17390182	2L_17390182_SNP [dm3] 2L_17390182_SNP [dm6]	C	T	4.294e^-5	0.91	INTRON CLIP-190
2L	3992381	2L_3992381_SNP [dm3] 2L_3992381_SNP [dm6]	C	T	4.327e^-5	0.91	UPSTREAM fred INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	6279249	3R_6279249_SNP [dm3] 3R_10453527_SNP [dm6]	A	T	4.331e^-5	0.91	INTERGENIC
2R	8964195	2R_8964195_SNP [dm3] 2R_13076690_SNP [dm6]	T	C	4.348e^-5	0.91	INTRON Drl-2
X	6530243	X_6530243_SNP [dm3] X_6636210_SNP [dm6]	G	T	4.362e^-5	0.91	UPSTREAM CR44817 DOWNSTREAM CG14443 INTRON pigs
3R	23670682	3R_23670682_SNP [dm3] 3R_27844960_SNP [dm6]	T	C	4.362e^-5	0.91	UPSTREAM Or98P & 1 other INTRON CG34353
2R	19034513	2R_19034513_SNP [dm3] 2R_23146990_SNP [dm6]	A	C	4.418e^-5	0.91	INTERGENIC	TF binding site mE1_TFBS_sbb
3R	23670560	3R_23670560_DEL [dm3] 3R_27844838_DEL [dm6]	GG	G	4.493e^-5	0.91	UPSTREAM Or98P INTRON CG34353
4	229842	4_229842_SNP [dm3] 4_209216_SNP [dm6]	A	T	4.555e^-5	0.91	INTERGENIC	transposable element FlyBase
2L	1948750	2L_1948750_SNP [dm3] 2L_1948750_SNP [dm6]	T	A	4.590e^-5	0.91	INTERGENIC	regulatory region REDfly_CRMs
2L	15807256	2L_15807256_SNP [dm3] 2L_15807256_SNP [dm6]	C	A	4.741e^-5	0.91	EXON CR44602
2R	10031189	2R_10031189_SNP [dm3] 2R_14143684_SNP [dm6]	C	T	4.773e^-5	0.91	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	10351375	3R_10351375_SNP [dm3] 3R_14525653_SNP [dm6]	T	C	4.783e^-5	0.91	INTRON Pde6
3R	10349630	3R_10349630_SNP [dm3] 3R_14523908_SNP [dm6]	T	C	4.814e^-5	0.91	DOWNSTREAM Cyp313a1 INTRON Pde6
X	2853800	X_2853800_SNP [dm3] X_2959767_SNP [dm6]	T	C	4.824e^-5	0.91	INTRON kirre & 1 other	TF binding site mE1_TFBS_Kr
3R	23781813	3R_23781813_SNP [dm3] 3R_27956091_SNP [dm6]	G	C	4.887e^-5	0.91	SYNONYMOUS_CODING CG5527	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11072204	2L_11072204_SNP [dm3] 2L_11072204_SNP [dm6]	A	G	4.997e^-5	0.91	DOWNSTREAM CG14915 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	8363723	3R_8363723_SNP [dm3] 3R_12538001_SNP [dm6]	T	G	5.059e^-5	0.91	INTRON Octbeta3R
X	18331829	X_18331829_SNP [dm3] X_18437796_SNP [dm6]	T	A	5.091e^-5	0.91	NON_SYNONYMOUS_CODING CG6290 UPSTREAM CG32548 INTRON CG32548	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
2L	14307071	2L_14307071_SNP [dm3] 2L_14307071_SNP [dm6]	T	C	5.200e^-5	0.91	INTRON wb
2R	10214793	2R_10214793_SNP [dm3] 2R_14327288_SNP [dm6]	T	C	5.205e^-5	0.91	INTRON Shroom	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10135227	2R_10135227_SNP [dm3] 2R_14247722_SNP [dm6]	T	G	5.262e^-5	0.91	INTRON Mdr50
2L	22035258	2L_22035258_DEL [dm3] 2L_22035258_DEL [dm6]	GCGATCCCAGCTCGACGTAC...	TG	5.293e^-5	0.91	INTERGENIC
2R	10134851	2R_10134851_DEL [dm3] 2R_14247346_DEL [dm6]	AA	A	5.318e^-5	0.91	INTRON Mdr50
2R	9098221	2R_9098221_SNP [dm3] 2R_13210716_SNP [dm6]	G	A	5.336e^-5	0.91	DOWNSTREAM FLASH INTRON CG34312 & 2 others
3R	7673870	3R_7673870_SNP [dm3] 3R_11848148_SNP [dm6]	C	T	5.342e^-5	0.91	INTRON CG6959	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	17386039	2L_17386039_SNP [dm3] 2L_17386039_SNP [dm6]	G	A	5.476e^-5	0.91	UPSTREAM CLIP-190 INTRON CLIP-190	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8966242	2R_8966242_SNP [dm3] 2R_13078737_SNP [dm6]	A	G	5.570e^-5	0.91	INTRON Drl-2
3R	21956146	3R_21956146_SNP [dm3] 3R_26130424_SNP [dm6]	G	C	5.584e^-5	0.91	UTR_3_PRIME CG31324 DOWNSTREAM CG31324
2L	17394922	2L_17394922_SNP [dm3] 2L_17394922_SNP [dm6]	T	A	5.643e^-5	0.91	INTRON CLIP-190
2L	17385080	2L_17385080_DEL [dm3] 2L_17385080_DEL [dm6]	AA	A	5.781e^-5	0.91	UTR_5_PRIME CLIP-190 UPSTREAM Lrch INTRON CLIP-190	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	14399177	2R_14399177_SNP [dm3] 2R_18511672_SNP [dm6]	A	C	5.820e^-5	0.91	INTERGENIC
3R	26200434	3R_26200434_SNP [dm3] 3R_30374712_SNP [dm6]	T	C	5.826e^-5	0.91	INTERGENIC

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=3.720e^-10)
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_2R_NS	0.06991

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	4.951	0.0841

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1947 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	16178623	2R_16178623_SNP [dm3] 2R_20291118_SNP [dm6]	G	T	2.500e^-7	0.469	DOWNSTREAM CkIIbeta2 INTRON Cpr56F
3L	4947200	3L_4947200_SNP [dm3] 3L_4947200_SNP [dm6]	A	T	6.233e^-7	0.584	INTRON Con
X	8182283	X_8182283_SNP [dm3] X_8288250_SNP [dm6]	A	T	1.414e^-6	0.678	INTRON nAChRalpha3
2R	4799432	2R_4799432_SNP [dm3] 2R_8911927_SNP [dm6]	C	T	1.445e^-6	0.678	NON_SYNONYMOUS_CODING Pgi	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	16178648	2R_16178648_SNP [dm3] 2R_20291143_SNP [dm6]	A	G	1.873e^-6	0.678	DOWNSTREAM CkIIbeta2 INTRON Cpr56F
3R	7532204	3R_7532204_SNP [dm3] 3R_11706482_SNP [dm6]	C	T	2.355e^-6	0.678	INTERGENIC
3R	7532214	3R_7532214_SNP [dm3] 3R_11706492_SNP [dm6]	G	C	2.580e^-6	0.678	INTERGENIC
3R	9943073	3R_9943073_SNP [dm3] 3R_14117351_SNP [dm6]	C	G	3.235e^-6	0.678	INTRON Kif19A
X	8182276	X_8182276_SNP [dm3] X_8288243_SNP [dm6]	C	G	3.255e^-6	0.678	INTRON nAChRalpha3
2R	11972378	2R_11972378_SNP [dm3] 2R_16084873_SNP [dm6]	A	C	3.976e^-6	0.746	NON_SYNONYMOUS_CODING Dg	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	23388917	3R_23388917_SNP [dm3] 3R_27563195_SNP [dm6]	C	T	5.265e^-6	0.768	UTR_3_PRIME wdb
3L	13632457	3L_13632457_SNP [dm3] 3L_13639357_SNP [dm6]	T	C	5.269e^-6	0.768	INTRON bru-3
X	8184377	X_8184377_SNP [dm3] X_8290344_SNP [dm6]	C	T	5.411e^-6	0.768	INTRON nAChRalpha3
2L	12056141	2L_12056141_SNP [dm3] 2L_12056141_SNP [dm6]	A	C	5.732e^-6	0.768	UPSTREAM RpL7-like & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl
X	15419512	X_15419512_SNP [dm3] X_15525479_SNP [dm6]	A	G	6.274e^-6	0.784	INTRON Ac13E
X	11288286	X_11288286_SNP [dm3] X_11394253_SNP [dm6]	C	G	7.239e^-6	0.819	SPLICE_SITE_REGION dlg1 INTRON dlg1
3L	17307470	3L_17307470_SNP [dm3] 3L_17314370_SNP [dm6]	G	C	7.659e^-6	0.819	UPSTREAM mir-219 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	8182278	X_8182278_SNP [dm3] X_8288245_SNP [dm6]	C	T	8.025e^-6	0.819	INTRON nAChRalpha3
2R	4801850	2R_4801850_SNP [dm3] 2R_8914345_SNP [dm6]	T	C	9.285e^-6	0.819	UPSTREAM lin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_run mE1_TFBS_Stat92E mE1_TFBS_Ubx
3L	4943538	3L_4943538_SNP [dm3] 3L_4943538_SNP [dm6]	G	A	1.025e^-5	0.819	INTRON Con
3R	26668172	3R_26668172_SNP [dm3] 3R_30842450_SNP [dm6]	C	T	1.072e^-5	0.819	DOWNSTREAM CG15544 INTERGENIC	TF binding site mE1_TFBS_cad
2R	9809831	2R_9809831_SNP [dm3] 2R_13922326_SNP [dm6]	G	A	1.123e^-5	0.819	INTRON shot
3L	12343488	3L_12343488_SNP [dm3] 3L_12350388_SNP [dm6]	T	C	1.124e^-5	0.819	INTRON CrzR
3L	1361975	3L_1361975_SNP [dm3] 3L_1361975_SNP [dm6]	G	A	1.152e^-5	0.819	INTRON Ptp61F
3L	1944499	3L_1944499_SNP [dm3] 3L_1944499_SNP [dm6]	G	T	1.197e^-5	0.819	NON_SYNONYMOUS_CODING mu2
X	5613330	X_5613330_SNP [dm3] X_5719297_SNP [dm6]	T	A	1.218e^-5	0.819	DOWNSTREAM CG32758 INTERGENIC
2R	4682739	2R_4682739_SNP [dm3] 2R_8795234_SNP [dm6]	G	A	1.278e^-5	0.819	INTERGENIC
3R	17708407	3R_17708407_SNP [dm3] 3R_21882685_SNP [dm6]	T	G	1.304e^-5	0.819	NON_SYNONYMOUS_CODING CG31465 EXON CR45046
2L	12056138	2L_12056138_SNP [dm3] 2L_12056138_SNP [dm6]	G	A	1.309e^-5	0.819	UPSTREAM RpL7-like & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl
3R	18692062	3R_18692062_MNP [dm3] 3R_22866340_MNP [dm6]	AGA	GAG	1.310e^-5	0.819	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14258019	3R_14258019_SNP [dm3] 3R_18432297_SNP [dm6]	A	T	1.421e^-5	0.826	INTRON fru
2R	10030838	2R_10030838_SNP [dm3] 2R_14143333_SNP [dm6]	G	A	1.452e^-5	0.826	INTERGENIC	TF binding site mE1_TFBS_bab1
2R	703729	2R_703729_SNP [dm3] 2R_4816224_SNP [dm6]	C	G	1.453e^-5	0.826	UTR_3_PRIME CG17528	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	1397614	3L_1397614_SNP [dm3] 3L_1397614_SNP [dm6]	A	G	1.500e^-5	0.827	UPSTREAM tRNA:E4:62Aa & 4 others INTRON Ptp61F
X	12593371	X_12593371_SNP [dm3] X_12699338_SNP [dm6]	G	A	1.639e^-5	0.831	INTRON Smr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	12850389	3L_12850389_SNP [dm3] 3L_12857289_SNP [dm6]	G	T	1.640e^-5	0.831	UTR_3_PRIME Ent3 & 1 other DOWNSTREAM Ent3	TF binding site mE1_TFBS_kn
3L	15910644	3L_15910644_SNP [dm3] 3L_15917544_SNP [dm6]	A	G	1.682e^-5	0.831	INTRON sff
2R	8702557	2R_8702557_SNP [dm3] 2R_12815052_SNP [dm6]	G	A	1.685e^-5	0.831	INTERGENIC
X	8182150	X_8182150_SNP [dm3] X_8288117_SNP [dm6]	G	T	1.762e^-5	0.831	INTRON nAChRalpha3
3R	25850804	3R_25850804_SNP [dm3] 3R_30025082_SNP [dm6]	C	T	1.786e^-5	0.831	INTRON Axn
3L	3837741	3L_3837741_SNP [dm3] 3L_3837741_SNP [dm6]	A	C	1.844e^-5	0.831	SYNONYMOUS_CODING enc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	4374652	X_4374652_SNP [dm3] X_4480619_SNP [dm6]	T	G	1.983e^-5	0.831	INTRON CR32773 & 1 other
2R	19045180	2R_19045180_SNP [dm3] 2R_23157657_SNP [dm6]	A	G	2.010e^-5	0.831	UTR_3_PRIME CG13545 INTRON CG9899
X	8182260	X_8182260_SNP [dm3] X_8288227_SNP [dm6]	G	T	2.033e^-5	0.831	INTRON nAChRalpha3
2R	11972352	2R_11972352_SNP [dm3] 2R_16084847_SNP [dm6]	A	T	2.039e^-5	0.831	SYNONYMOUS_CODING Dg	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	18692184	3R_18692184_SNP [dm3] 3R_22866462_SNP [dm6]	T	A	2.129e^-5	0.831	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14644477	3L_14644477_SNP [dm3] 3L_14651377_SNP [dm6]	C	T	2.158e^-5	0.831	INTRON dlp	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
2R	6540696	2R_6540696_SNP [dm3] 2R_10653191_SNP [dm6]	A	C	2.170e^-5	0.831	INTERGENIC
3L	1944502	3L_1944502_SNP [dm3] 3L_1944502_SNP [dm6]	C	T	2.172e^-5	0.831	SYNONYMOUS_CODING mu2
X	4242574	X_4242574_SNP [dm3] X_4348541_SNP [dm6]	G	C	2.216e^-5	0.831	INTRON norpA
2L	4983906	2L_4983906_SNP [dm3] 2L_4983906_SNP [dm6]	A	C	2.344e^-5	0.862	SYNONYMOUS_CODING CG34126	TF binding site mE1_TFBS_chinmo
X	8184385	X_8184385_SNP [dm3] X_8290352_SNP [dm6]	G	T	2.452e^-5	0.878	INTRON nAChRalpha3
2L	2711970	2L_2711970_SNP [dm3] 2L_2711970_SNP [dm6]	G	A	2.544e^-5	0.878	INTRON CG31690	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	6563351	3L_6563351_SNP [dm3] 3L_6570251_SNP [dm6]	T	C	2.556e^-5	0.878	INTRON CG18769 & 1 other
3R	4251383	3R_4251383_SNP [dm3] 3R_8425661_SNP [dm6]	A	G	2.628e^-5	0.878	INTRON CG45263
3L	1951632	3L_1951632_SNP [dm3] 3L_1951632_SNP [dm6]	T	C	2.685e^-5	0.878	NON_SYNONYMOUS_CODING mv	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	15807256	2L_15807256_SNP [dm3] 2L_15807256_SNP [dm6]	C	A	2.701e^-5	0.878	EXON CR44602
3L	1399790	3L_1399790_SNP [dm3] 3L_1399790_SNP [dm6]	G	A	2.797e^-5	0.878	SYNONYMOUS_CODING CG32320 INTRON Ptp61F
X	13503117	X_13503117_SNP [dm3] X_13609084_SNP [dm6]	C	T	2.821e^-5	0.878	UTR_3_PRIME CG11178 DOWNSTREAM Ndc80
3L	4941841	3L_4941841_SNP [dm3] 3L_4941841_SNP [dm6]	T	C	2.843e^-5	0.878	INTRON Con
3R	18692018	3R_18692018_SNP [dm3] 3R_22866296_SNP [dm6]	A	C	2.855e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19118629	X_19118629_SNP [dm3] X_19224596_SNP [dm6]	G	T	2.911e^-5	0.88	INTRON CG7884	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	10030846	2R_10030846_INS [dm3] 2R_14143341_INS [dm6]	A	ATTTTACAAGGTGACATCTT...	3.036e^-5	0.893	INTERGENIC	TF binding site mE1_TFBS_bab1
3L	1952407	3L_1952407_SNP [dm3] 3L_1952407_SNP [dm6]	T	C	3.081e^-5	0.893	SYNONYMOUS_CODING mv	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	12056075	2L_12056075_SNP [dm3] 2L_12056075_SNP [dm6]	G	A	3.144e^-5	0.893	UPSTREAM RpL7-like & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl
2L	12056027	2L_12056027_SNP [dm3] 2L_12056027_SNP [dm6]	A	C	3.164e^-5	0.893	UTR_5_PRIME JhI-21 UPSTREAM RpL7-like & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	1745046	3L_1745046_SNP [dm3] 3L_1745046_SNP [dm6]	A	C	3.225e^-5	0.893	UTR_3_PRIME Gk	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	15997437	2L_15997437_SNP [dm3] 2L_15997437_SNP [dm6]	A	G	3.237e^-5	0.893	INTERGENIC
2L	15488041	2L_15488041_SNP [dm3] 2L_15488041_SNP [dm6]	C	T	3.289e^-5	0.894	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	2603342	2L_2603342_SNP [dm3] 2L_2603342_SNP [dm6]	C	T	3.454e^-5	0.923	INTERGENIC
2R	15572890	2R_15572890_SNP [dm3] 2R_19685385_SNP [dm6]	C	T	3.496e^-5	0.923	DOWNSTREAM CG15128 INTERGENIC
X	2525018	X_2525018_SNP [dm3] X_2630985_SNP [dm6]	C	T	3.571e^-5	0.926	SYNONYMOUS_CODING PI4KIIIalpha	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12850391	3L_12850391_SNP [dm3] 3L_12857291_SNP [dm6]	A	T	3.624e^-5	0.926	UTR_3_PRIME Ent3 & 1 other DOWNSTREAM Ent3	TF binding site mE1_TFBS_kn
3L	16256939	3L_16256939_SNP [dm3] 3L_16263839_SNP [dm6]	G	T	3.782e^-5	0.926	NON_SYNONYMOUS_CODING CG13070 DOWNSTREAM CG13071 & 1 other
2R	19045049	2R_19045049_SNP [dm3] 2R_23157526_SNP [dm6]	A	G	3.790e^-5	0.926	DOWNSTREAM CG13545 INTRON CG9899
3L	10745229	3L_10745229_SNP [dm3] 3L_10752129_SNP [dm6]	G	A	3.825e^-5	0.926	INTERGENIC
3R	8975322	3R_8975322_SNP [dm3] 3R_13149600_SNP [dm6]	A	C	3.977e^-5	0.926	INTRON timeout & 2 others	TF binding site BDTNP1_TFBS_twi
3L	13632458	3L_13632458_SNP [dm3] 3L_13639358_SNP [dm6]	G	A	3.984e^-5	0.926	INTRON bru-3
X	19118631	X_19118631_INS [dm3] X_19224598_INS [dm6]	G	GT	4.014e^-5	0.926	INTRON CG7884	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	8379920	3R_8379920_SNP [dm3] 3R_12554198_SNP [dm6]	T	C	4.035e^-5	0.926	INTRON Octbeta2R
2R	21020619	2R_21020619_SNP [dm3] 2R_25133096_SNP [dm6]	C	T	4.152e^-5	0.926	INTRON lov	transposable element FlyBase
X	13503116	X_13503116_SNP [dm3] X_13609083_SNP [dm6]	A	T	4.204e^-5	0.926	UTR_3_PRIME CG11178 DOWNSTREAM Ndc80
3R	7592851	3R_7592851_INS [dm3] 3R_11767129_INS [dm6]	G	GGAA	4.377e^-5	0.926	UTR_3_PRIME l_3_neo38
2R	9810120	2R_9810120_SNP [dm3] 2R_13922615_SNP [dm6]	C	T	4.384e^-5	0.926	INTRON shot
2R	10998501	2R_10998501_SNP [dm3] 2R_15110996_SNP [dm6]	T	G	4.422e^-5	0.926	INTERGENIC
X	12880717	X_12880717_SNP [dm3] X_12986684_SNP [dm6]	G	T	4.437e^-5	0.926	INTERGENIC
3L	10745165	3L_10745165_SNP [dm3] 3L_10752065_SNP [dm6]	T	A	4.486e^-5	0.926	INTERGENIC
2R	10510771	2R_10510771_SNP [dm3] 2R_14623266_SNP [dm6]	C	T	4.545e^-5	0.926	UPSTREAM snoRNA:Me28S-A992 & 4 others DOWNSTREAM snoRNA:Me28S-C3227b & 3 others INTRON Uhg5	TF binding site mE1_TFBS_zfh1
3R	8975342	3R_8975342_SNP [dm3] 3R_13149620_SNP [dm6]	G	A	4.575e^-5	0.926	INTRON timeout & 2 others	TF binding site BDTNP1_TFBS_twi
2L	10086590	2L_10086590_SNP [dm3] 2L_10086590_SNP [dm6]	A	C	4.588e^-5	0.926	INTRON CG44153
3L	9856765	3L_9856765_SNP [dm3] 3L_9863665_SNP [dm6]	C	G	4.764e^-5	0.926	UPSTREAM CG8108 INTRON iPLA2-VIA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	14644200	3L_14644200_SNP [dm3] 3L_14651100_SNP [dm6]	C	T	4.809e^-5	0.926	INTRON dlp	TF binding site mE1_TFBS_cnc
2R	10002034	2R_10002034_SNP [dm3] 2R_14114529_SNP [dm6]	C	A	4.906e^-5	0.926	INTRON Prosap	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	1033895	3L_1033895_SNP [dm3] 3L_1033895_SNP [dm6]	C	T	4.948e^-5	0.926	UTR_5_PRIME trio UPSTREAM CG9205	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco
3R	23388844	3R_23388844_DEL [dm3] 3R_27563122_DEL [dm6]	TT	T	5.042e^-5	0.926	UTR_3_PRIME wdb
2L	7636772	2L_7636772_SNP [dm3] 2L_7636772_SNP [dm6]	T	C	5.092e^-5	0.926	UPSTREAM CR44800 DOWNSTREAM CR44799 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	9691301	3R_9691301_SNP [dm3] 3R_13865579_SNP [dm6]	C	T	5.099e^-5	0.926	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2R	10029833	2R_10029833_SNP [dm3] 2R_14142328_SNP [dm6]	C	G	5.173e^-5	0.926	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_ttk
X	12593377	X_12593377_SNP [dm3] X_12699344_SNP [dm6]	G	T	5.255e^-5	0.926	INTRON Smr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	8182250	X_8182250_SNP [dm3] X_8288217_SNP [dm6]	C	A	5.274e^-5	0.926	INTRON nAChRalpha3

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By genomic position
Variant impact
Gene name

cv_SleepLength_Day phenotype

Phenotype distribution and association to known covariates

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Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results