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=5.936e^-6)
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	0.025256
In_3R_P	0.020479
In_3R_K	0.007535

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	6.5313	0.0382
In_3R_K	11.9577	0.0025

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3948 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	18737270	X_18737270_SNP [dm3] X_18843237_SNP [dm6]	G	A	1.699e^-7	0.109	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3R	5000946	3R_5000946_INS [dm3] 3R_9175224_INS [dm6]	A	AA	2.605e^-7	0.109	INTRON pum
X	18173928	X_18173928_SNP [dm3] X_18279895_SNP [dm6]	G	T	3.380e^-7	0.109	INTRON upd3	TF binding site mE1_TFBS_chinmo
3L	22373749	3L_22373749_SNP [dm3] 3L_22380649_SNP [dm6]	G	C	3.651e^-7	0.109	INTRON Ten-m	TF binding site mE1_TFBS_sens
3R	4996216	3R_4996216_SNP [dm3] 3R_9170494_SNP [dm6]	T	C	4.048e^-7	0.109	INTRON pum
3R	4995451	3R_4995451_SNP [dm3] 3R_9169729_SNP [dm6]	T	C	4.606e^-7	0.109	INTRON pum
3R	5000941	3R_5000941_MNP [dm3] 3R_9175219_MNP [dm6]	CTC	TCA	6.299e^-7	0.109	INTRON pum
3R	5000954	3R_5000954_DEL [dm3] 3R_9175232_DEL [dm6]	AA	A	7.015e^-7	0.109	INTRON pum
X	18173239	X_18173239_SNP [dm3] X_18279206_SNP [dm6]	G	A	8.109e^-7	0.109	INTRON upd3
3R	5001765	3R_5001765_SNP [dm3] 3R_9176043_SNP [dm6]	C	T	8.518e^-7	0.109	INTRON pum
3L	19969059	3L_19969059_SNP [dm3] 3L_19975959_SNP [dm6]	G	T	8.563e^-7	0.109	INTRON Ac76E
3R	4992367	3R_4992367_SNP [dm3] 3R_9166645_SNP [dm6]	A	T	9.379e^-7	0.109	INTRON pum
3R	5001093	3R_5001093_SNP [dm3] 3R_9175371_SNP [dm6]	A	G	9.809e^-7	0.109	INTRON pum
3R	4996564	3R_4996564_SNP [dm3] 3R_9170842_SNP [dm6]	G	A	1.004e^-6	0.109	INTRON pum
3R	5001468	3R_5001468_SNP [dm3] 3R_9175746_SNP [dm6]	C	A	1.005e^-6	0.109	INTRON pum
3R	4997466	3R_4997466_SNP [dm3] 3R_9171744_SNP [dm6]	A	T	1.030e^-6	0.109	INTRON pum
3R	8366414	3R_8366414_SNP [dm3] 3R_12540692_SNP [dm6]	C	A	1.069e^-6	0.109	INTRON Octbeta3R
2L	6035309	2L_6035309_SNP [dm3] 2L_6035309_SNP [dm6]	G	C	1.161e^-6	0.109	SYNONYMOUS_CODING mtm UPSTREAM CG9109	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	4998854	3R_4998854_SNP [dm3] 3R_9173132_SNP [dm6]	A	G	1.174e^-6	0.109	INTRON pum
3R	13186623	3R_13186623_SNP [dm3] 3R_17360901_SNP [dm6]	G	A	1.193e^-6	0.109	INTRON beat-IIa
3R	5001114	3R_5001114_SNP [dm3] 3R_9175392_SNP [dm6]	C	A	1.266e^-6	0.109	INTRON pum
X	16018200	X_16018200_SNP [dm3] X_16124167_SNP [dm6]	A	T	1.306e^-6	0.109	UTR_5_PRIME disco-r INTRON disco-r	TF binding site mE1_TFBS_inv
3L	17025185	3L_17025185_SNP [dm3] 3L_17032085_SNP [dm6]	C	G	1.331e^-6	0.109	UPSTREAM Ilp8 EXON CR45756	TF binding site mE1_TFBS_Trl
3R	5000921	3R_5000921_SNP [dm3] 3R_9175199_SNP [dm6]	C	A	1.426e^-6	0.111	INTRON pum	TF binding site mE1_TFBS_bab1
3R	22283050	3R_22283050_SNP [dm3] 3R_26457328_SNP [dm6]	T	A	1.685e^-6	0.126	UPSTREAM CG14238 DOWNSTREAM CG14237 INTERGENIC
2L	9972740	2L_9972740_SNP [dm3] 2L_9972740_SNP [dm6]	A	G	1.988e^-6	0.142	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	18737232	X_18737232_SNP [dm3] X_18843199_SNP [dm6]	T	G	2.044e^-6	0.142	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18173144	X_18173144_SNP [dm3] X_18279111_SNP [dm6]	G	A	2.515e^-6	0.165	INTRON upd3
3L	6570565	3L_6570565_SNP [dm3] 3L_6577465_SNP [dm6]	T	C	2.655e^-6	0.165	INTRON CG18769 & 1 other
2L	10008429	2L_10008429_INS [dm3] 2L_10008429_INS [dm6]	T	AA	2.794e^-6	0.165	UTR_3_PRIME CG4747 UPSTREAM Trp1 DOWNSTREAM CG4747
3R	4998137	3R_4998137_SNP [dm3] 3R_9172415_SNP [dm6]	T	A	2.823e^-6	0.165	INTRON pum	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	5002903	3R_5002903_SNP [dm3] 3R_9177181_SNP [dm6]	T	G	3.360e^-6	0.165	UPSTREAM CG11997 INTRON pum	TF binding site BDTNP1_TFBS_twi
X	18737224	X_18737224_SNP [dm3] X_18843191_SNP [dm6]	A	C	3.544e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
2L	16813657	2L_16813657_SNP [dm3] 2L_16813657_SNP [dm6]	T	C	3.642e^-6	0.165	SYNONYMOUS_CODING CG13272 INTRON CG13280
3R	10193750	3R_10193750_SNP [dm3] 3R_14368028_SNP [dm6]	G	T	3.705e^-6	0.165	INTRON NK7.1
3R	25817054	3R_25817054_SNP [dm3] 3R_29991332_SNP [dm6]	G	A	3.735e^-6	0.165	UTR_3_PRIME Acph-1 DOWNSTREAM CG7896	TF binding site mE1_TFBS_cad
3R	5001233	3R_5001233_SNP [dm3] 3R_9175511_SNP [dm6]	C	G	3.752e^-6	0.165	INTRON pum
X	18737157	X_18737157_SNP [dm3] X_18843124_SNP [dm6]	A	G	4.032e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737165	X_18737165_SNP [dm3] X_18843132_SNP [dm6]	A	T	4.055e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
3R	5000901	3R_5000901_SNP [dm3] 3R_9175179_SNP [dm6]	T	C	4.092e^-6	0.165	INTRON pum	TF binding site mE1_TFBS_bab1
3R	13647569	3R_13647569_SNP [dm3] 3R_17821847_SNP [dm6]	A	G	4.118e^-6	0.165	INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
X	18737255	X_18737255_SNP [dm3] X_18843222_SNP [dm6]	A	T	4.198e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737023	X_18737023_SNP [dm3] X_18842990_SNP [dm6]	T	G	4.302e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737171	X_18737171_SNP [dm3] X_18843138_SNP [dm6]	C	A	4.410e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737254	X_18737254_SNP [dm3] X_18843221_SNP [dm6]	T	C	4.715e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3R	4995330	3R_4995330_SNP [dm3] 3R_9169608_SNP [dm6]	A	G	4.761e^-6	0.165	INTRON pum
X	18173959	X_18173959_SNP [dm3] X_18279926_SNP [dm6]	T	A	4.890e^-6	0.165	INTRON upd3
3R	14732739	3R_14732739_SNP [dm3] 3R_18907017_SNP [dm6]	A	C	4.914e^-6	0.165	UTR_5_PRIME EndoA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2R	19057208	2R_19057208_SNP [dm3] 2R_23169685_SNP [dm6]	C	A	5.097e^-6	0.165	INTRON CG34371	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	18737168	X_18737168_SNP [dm3] X_18843135_SNP [dm6]	C	G	5.306e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737175	X_18737175_SNP [dm3] X_18843142_SNP [dm6]	C	G	5.306e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
X	18737252	X_18737252_SNP [dm3] X_18843219_SNP [dm6]	T	A	5.306e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737207	X_18737207_SNP [dm3] X_18843174_SNP [dm6]	C	T	5.417e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
X	18737186	X_18737186_SNP [dm3] X_18843153_SNP [dm6]	A	G	5.418e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
X	18737240	X_18737240_SNP [dm3] X_18843207_SNP [dm6]	A	T	5.418e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737234	X_18737234_SNP [dm3] X_18843201_SNP [dm6]	T	C	5.463e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3L	7022263	3L_7022263_SNP [dm3] 3L_7029163_SNP [dm6]	C	G	5.569e^-6	0.165	INTRON Mp
X	18737163	X_18737163_SNP [dm3] X_18843130_SNP [dm6]	A	T	5.680e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737250	X_18737250_INS [dm3] X_18843217_INS [dm6]	A	ATCTGTATGCTG...	5.707e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	9318056	X_9318056_SNP [dm3] X_9424023_SNP [dm6]	C	G	5.727e^-6	0.165	INTRON mgl
3R	10224232	3R_10224232_SNP [dm3] 3R_14398510_SNP [dm6]	G	A	5.796e^-6	0.165	INTRON cv-c
2R	11250394	2R_11250394_SNP [dm3] 2R_15362889_SNP [dm6]	A	G	5.827e^-6	0.165	INTRON unc-5
X	18737227	X_18737227_SNP [dm3] X_18843194_SNP [dm6]	A	T	5.907e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737229	X_18737229_SNP [dm3] X_18843196_SNP [dm6]	A	T	5.907e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3R	5001118	3R_5001118_SNP [dm3] 3R_9175396_SNP [dm6]	T	C	5.950e^-6	0.165	INTRON pum
2L	19624712	2L_19624712_DEL [dm3] 2L_19624712_DEL [dm6]	GGTCGTG	G	6.024e^-6	0.165	INTRON Lar
X	19652156	X_19652156_SNP [dm3] X_19758123_SNP [dm6]	C	T	6.188e^-6	0.165	SYNONYMOUS_CODING Pmp70	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	18737019	X_18737019_SNP [dm3] X_18842986_SNP [dm6]	G	C	6.267e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737156	X_18737156_SNP [dm3] X_18843123_SNP [dm6]	A	T	6.286e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737238	X_18737238_SNP [dm3] X_18843205_SNP [dm6]	C	A	6.298e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3R	10057286	3R_10057286_SNP [dm3] 3R_14231564_SNP [dm6]	C	A	6.382e^-6	0.165	INTERGENIC
X	18737202	X_18737202_INS [dm3] X_18843169_INS [dm6]	TA	CGTGTGGCTTGT...	6.408e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3R	5000898	3R_5000898_SNP [dm3] 3R_9175176_SNP [dm6]	A	G	6.464e^-6	0.165	INTRON pum	TF binding site mE1_TFBS_bab1
2R	4085987	2R_4085987_SNP [dm3] 2R_8198482_SNP [dm6]	C	T	6.581e^-6	0.165	INTRON LRP1
X	18737241	X_18737241_SNP [dm3] X_18843208_SNP [dm6]	A	C	6.733e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737262	X_18737262_SNP [dm3] X_18843229_SNP [dm6]	A	G	6.741e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737017	X_18737017_SNP [dm3] X_18842984_SNP [dm6]	A	T	6.775e^-6	0.165	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737015	X_18737015_SNP [dm3] X_18842982_SNP [dm6]	A	T	7.269e^-6	0.169	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC
X	18737245	X_18737245_INS [dm3] X_18843212_INS [dm6]	A	TCTC	7.411e^-6	0.169	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3R	5000860	3R_5000860_DEL [dm3] 3R_9175138_DEL [dm6]	AAGACA	A	7.468e^-6	0.169	INTRON pum	TF binding site mE1_TFBS_bab1
2L	496826	2L_496826_SNP [dm3] 2L_496826_SNP [dm6]	G	C	7.478e^-6	0.169	INTRON ush	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	18615373	3R_18615373_SNP [dm3] 3R_22789651_SNP [dm6]	A	G	7.633e^-6	0.169	NON_SYNONYMOUS_CODING CG7029	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	13985639	X_13985639_DEL [dm3] X_14091606_DEL [dm6]	CTTGGCA	C	7.651e^-6	0.169	INTERGENIC
3R	5001499	3R_5001499_SNP [dm3] 3R_9175777_SNP [dm6]	A	C	7.676e^-6	0.169	INTRON pum
3R	5001032	3R_5001032_SNP [dm3] 3R_9175310_SNP [dm6]	A	T	7.769e^-6	0.169	INTRON pum
3R	5005254	3R_5005254_SNP [dm3] 3R_9179532_SNP [dm6]	G	A	7.847e^-6	0.169	DOWNSTREAM CG11997 INTRON pum
2R	11621431	2R_11621431_SNP [dm3] 2R_15733926_SNP [dm6]	T	A	7.895e^-6	0.169	INTRON CG30089
X	18737236	X_18737236_SNP [dm3] X_18843203_SNP [dm6]	G	A	7.929e^-6	0.169	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
X	18737260	X_18737260_SNP [dm3] X_18843227_SNP [dm6]	A	C	8.438e^-6	0.172	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
2L	7306552	2L_7306552_SNP [dm3] 2L_7306552_SNP [dm6]	A	T	8.591e^-6	0.172	UPSTREAM wg INTERGENIC	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco
3R	10057283	3R_10057283_SNP [dm3] 3R_14231561_SNP [dm6]	A	G	8.753e^-6	0.172	INTERGENIC
3L	10693440	3L_10693440_SNP [dm3] 3L_10700340_SNP [dm6]	T	G	8.791e^-6	0.172	INTERGENIC
2L	1187301	2L_1187301_SNP [dm3] 2L_1187301_SNP [dm6]	A	T	8.877e^-6	0.172	INTRON CG5001
3R	13647564	3R_13647564_INS [dm3] 3R_17821842_INS [dm6]	G	GC	8.899e^-6	0.172	INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3R	10159698	3R_10159698_SNP [dm3] 3R_14333976_SNP [dm6]	G	A	8.940e^-6	0.172	INTRON NK7.1
2L	14312926	2L_14312926_SNP [dm3] 2L_14312926_SNP [dm6]	C	T	9.034e^-6	0.172	INTRON wb
3L	14754938	3L_14754938_SNP [dm3] 3L_14761838_SNP [dm6]	C	G	9.065e^-6	0.172	UTR_5_PRIME CG33260 UPSTREAM CG9384 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7022275	3L_7022275_SNP [dm3] 3L_7029175_SNP [dm6]	A	G	9.085e^-6	0.172	INTRON Mp
X	18737090	X_18737090_DEL [dm3] X_18843057_DEL [dm6]	CCACGATTATCGCATACCCG...	C	9.102e^-6	0.172	UPSTREAM CG34422 DOWNSTREAM Pvf1 INTERGENIC	transposable element FlyBase
3L	7022204	3L_7022204_SNP [dm3] 3L_7029104_SNP [dm6]	C	A	9.175e^-6	0.172	INTRON Mp

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=1.635e^-11)
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	0.03411
In_3R_K	0.08429

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.5025	0.0142
In_3R_K	5.6946	0.058

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2742 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
2L	3101910	2L_3101910_SNP [dm3] 2L_3101910_SNP [dm6]	T	C	3.027e^-7	0.461	INTRON toc
3L	12630024	3L_12630024_INS [dm3] 3L_12636924_INS [dm6]	T	TT	7.428e^-7	0.461	INTRON CR32111
2L	14283269	2L_14283269_SNP [dm3] 2L_14283269_SNP [dm6]	C	T	8.985e^-7	0.461	INTRON wb	TF binding site BDTNP1_TFBS_da mE1_TFBS_h mE1_TFBS_HSA
3L	12630140	3L_12630140_INS [dm3] 3L_12637040_INS [dm6]	T	TTAGAT	1.049e^-6	0.461	INTRON CR32111
3L	12630109	3L_12630109_SNP [dm3] 3L_12637009_SNP [dm6]	C	T	1.504e^-6	0.461	INTRON CR32111
X	4117063	X_4117063_SNP [dm3] X_4223030_SNP [dm6]	T	C	1.875e^-6	0.461	SYNONYMOUS_CODING CG15570
2L	1964592	2L_1964592_SNP [dm3] 2L_1964592_SNP [dm6]	A	C	2.295e^-6	0.461	UPSTREAM tRNA:CR31942 INTRON erm	regulatory region REDfly_CRMs
3L	12630168	3L_12630168_SNP [dm3] 3L_12637068_SNP [dm6]	C	T	2.432e^-6	0.461	INTRON CR32111
3L	12630112	3L_12630112_SNP [dm3] 3L_12637012_SNP [dm6]	T	G	2.736e^-6	0.461	INTRON CR32111
X	19737673	X_19737673_SNP [dm3] X_19843640_SNP [dm6]	A	G	3.642e^-6	0.461	INTRON pico	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens
2R	15475221	2R_15475221_SNP [dm3] 2R_19587716_SNP [dm6]	C	G	3.674e^-6	0.461	UTR_3_PRIME CG42878 INTRON sm
2L	12726794	2L_12726794_SNP [dm3] 2L_12726794_SNP [dm6]	C	T	3.780e^-6	0.461	SYNONYMOUS_CODING MRP
3R	25061331	3R_25061331_SNP [dm3] 3R_29235609_SNP [dm6]	G	A	3.910e^-6	0.461	DOWNSTREAM CG15817 INTRON CG11951	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	11637450	2R_11637450_SNP [dm3] 2R_15749945_SNP [dm6]	C	A	3.998e^-6	0.461	INTRON CG30089
3R	10378520	3R_10378520_SNP [dm3] 3R_14552798_SNP [dm6]	T	C	4.216e^-6	0.461	INTRON Pde6
3R	24514206	3R_24514206_SNP [dm3] 3R_28688484_SNP [dm6]	G	T	4.243e^-6	0.461	INTRON CG9990
2L	8341464	2L_8341464_SNP [dm3] 2L_8341464_SNP [dm6]	T	C	4.663e^-6	0.461	UTR_3_PRIME CG14274
2L	494184	2L_494184_SNP [dm3] 2L_494184_SNP [dm6]	T	C	4.739e^-6	0.461	INTRON ush
2R	15475109	2R_15475109_SNP [dm3] 2R_19587604_SNP [dm6]	A	T	4.964e^-6	0.461	SYNONYMOUS_CODING CG42878 INTRON sm
2R	15475210	2R_15475210_SNP [dm3] 2R_19587705_SNP [dm6]	G	A	5.112e^-6	0.461	UTR_3_PRIME CG42878 INTRON sm
3R	15582957	3R_15582957_SNP [dm3] 3R_19757235_SNP [dm6]	G	A	5.388e^-6	0.461	INTRON GluClalpha
3R	24893367	3R_24893367_SNP [dm3] 3R_29067645_SNP [dm6]	T	C	5.405e^-6	0.461	INTRON CG11873	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	24514248	3R_24514248_SNP [dm3] 3R_28688526_SNP [dm6]	T	G	6.195e^-6	0.469	INTRON CG9990
3R	24893734	3R_24893734_SNP [dm3] 3R_29068012_SNP [dm6]	A	T	6.209e^-6	0.469	INTRON CG11873	TF binding site BDTNP1_TFBS_dl
3L	10377578	3L_10377578_SNP [dm3] 3L_10384478_SNP [dm6]	A	C	6.250e^-6	0.469	INTERGENIC
3R	8271680	3R_8271680_SNP [dm3] 3R_12445958_SNP [dm6]	A	G	7.532e^-6	0.502	INTRON Desat1
3L	21397522	3L_21397522_SNP [dm3] 3L_21404422_SNP [dm6]	C	T	8.042e^-6	0.502	INTRON rgn
2L	9169493	2L_9169493_SNP [dm3] 2L_9169493_SNP [dm6]	G	A	8.285e^-6	0.502	INTRON tai
2L	16470343	2L_16470343_DEL [dm3] 2L_16470343_DEL [dm6]	GG	G	8.374e^-6	0.502	INTRON dac	regulatory region REDfly_CRMs
2L	14278086	2L_14278086_SNP [dm3] 2L_14278086_SNP [dm6]	C	T	8.485e^-6	0.502	DOWNSTREAM CG32971 INTRON wb
2L	8341490	2L_8341490_SNP [dm3] 2L_8341490_SNP [dm6]	A	T	8.688e^-6	0.502	UTR_3_PRIME CG14274
2L	7984754	2L_7984754_SNP [dm3] 2L_7984754_SNP [dm6]	G	A	8.788e^-6	0.502	UTR_5_PRIME CG7231 UPSTREAM Snoo & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	11912956	3L_11912956_SNP [dm3] 3L_11919856_SNP [dm6]	G	T	8.842e^-6	0.502	INTRON CG44837
3R	17158006	3R_17158006_SNP [dm3] 3R_21332284_SNP [dm6]	C	T	9.106e^-6	0.502	INTRON CG16791	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	9197960	2L_9197960_SNP [dm3] 2L_9197960_SNP [dm6]	T	A	1.005e^-5	0.538	INTRON tai
3L	12630125	3L_12630125_SNP [dm3] 3L_12637025_SNP [dm6]	C	G	1.048e^-5	0.546	INTRON CR32111
2R	20365146	2R_20365146_SNP [dm3] 2R_24477623_SNP [dm6]	A	G	1.109e^-5	0.558	INTRON CG13579	TF binding site mE1_TFBS_chinmo
3R	22696172	3R_22696172_SNP [dm3] 3R_26870450_SNP [dm6]	A	G	1.131e^-5	0.558	INTRON BM-40-SPARC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	20358977	2R_20358977_SNP [dm3] 2R_24471454_SNP [dm6]	T	C	1.193e^-5	0.574	INTRON CG13579
X	14435561	X_14435561_SNP [dm3] X_14541528_SNP [dm6]	C	T	1.228e^-5	0.576	EXON CR45521
2L	4617180	2L_4617180_SNP [dm3] 2L_4617180_SNP [dm6]	T	G	1.282e^-5	0.586	INTERGENIC
3R	23019195	3R_23019195_SNP [dm3] 3R_27193473_SNP [dm6]	C	T	1.341e^-5	0.591	INTRON Ser	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2L	3176107	2L_3176107_SNP [dm3] 2L_3176107_SNP [dm6]	G	T	1.400e^-5	0.591	INTRON CG34393
3R	18971533	3R_18971533_SNP [dm3] 3R_23145811_SNP [dm6]	G	T	1.424e^-5	0.591	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E
3L	2808187	3L_2808187_SNP [dm3] 3L_2808187_SNP [dm6]	A	G	1.487e^-5	0.591	INTRON CG43444	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	7582571	X_7582571_SNP [dm3] X_7688538_SNP [dm6]	G	A	1.673e^-5	0.591	SYNONYMOUS_CODING CHES-1-like	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
3R	25909513	3R_25909513_SNP [dm3] 3R_30083791_SNP [dm6]	G	T	1.708e^-5	0.591	INTRON sima
3R	9686170	3R_9686170_SNP [dm3] 3R_13860448_SNP [dm6]	C	G	1.715e^-5	0.591	INTERGENIC
2L	577966	2L_577966_SNP [dm3] 2L_577966_SNP [dm6]	T	C	1.733e^-5	0.591	UTR_5_PRIME Pph13	TF binding site mE1_TFBS_cad
3L	10377566	3L_10377566_SNP [dm3] 3L_10384466_SNP [dm6]	A	C	1.802e^-5	0.591	INTERGENIC
2R	18005133	2R_18005133_SNP [dm3] 2R_22117628_SNP [dm6]	A	C	1.871e^-5	0.591	INTRON Vrp1
X	12820358	X_12820358_SNP [dm3] X_12926325_SNP [dm6]	T	A	1.991e^-5	0.591	INTRON fne	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	1931658	2L_1931658_SNP [dm3] 2L_1931658_SNP [dm6]	G	C	2.122e^-5	0.591	INTRON CG7337
2R	9203492	2R_9203492_SNP [dm3] 2R_13315987_SNP [dm6]	G	A	2.139e^-5	0.591	INTERGENIC
3L	14709758	3L_14709758_SNP [dm3] 3L_14716658_SNP [dm6]	T	C	2.210e^-5	0.591	INTRON ome	regulatory region REDfly_CRMs
2L	14918236	2L_14918236_SNP [dm3] 2L_14918236_SNP [dm6]	T	A	2.214e^-5	0.591	INTRON CG42313
3L	10378565	3L_10378565_SNP [dm3] 3L_10385465_SNP [dm6]	G	A	2.261e^-5	0.591	UPSTREAM CR45245 INTERGENIC
2L	12722329	2L_12722329_SNP [dm3] 2L_12722329_SNP [dm6]	C	G	2.278e^-5	0.591	START_GAINED MRP UTR_5_PRIME MRP UPSTREAM CG5792 INTRON MRP	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	12555208	2L_12555208_SNP [dm3] 2L_12555208_SNP [dm6]	G	A	2.328e^-5	0.591	INTERGENIC
X	20219354	X_20219354_SNP [dm3] X_20348327_SNP [dm6]	G	C	2.337e^-5	0.591	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	4839089	X_4839089_SNP [dm3] X_4945056_SNP [dm6]	A	G	2.404e^-5	0.591	INTRON Ptp4E
3R	23052589	3R_23052589_SNP [dm3] 3R_27226867_SNP [dm6]	G	T	2.417e^-5	0.591	DOWNSTREAM CG42813 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	14282010	2L_14282010_SNP [dm3] 2L_14282010_SNP [dm6]	C	T	2.423e^-5	0.591	INTRON wb	TF binding site mE1_TFBS_cad
3L	16924626	3L_16924626_SNP [dm3] 3L_16931526_SNP [dm6]	A	T	2.440e^-5	0.591	SYNONYMOUS_CODING CG11905 INTRON CG11905	TF binding site mE1_TFBS_chinmo
3R	15591834	3R_15591834_SNP [dm3] 3R_19766112_SNP [dm6]	A	T	2.451e^-5	0.591	INTRON GluClalpha
2L	14290209	2L_14290209_SNP [dm3] 2L_14290209_SNP [dm6]	C	T	2.501e^-5	0.591	UPSTREAM CR43639 INTRON wb	TF binding site mE1_TFBS_chinmo
2L	577967	2L_577967_SNP [dm3] 2L_577967_SNP [dm6]	T	C	2.683e^-5	0.591	UTR_5_PRIME Pph13	TF binding site mE1_TFBS_cad
3R	16596148	3R_16596148_SNP [dm3] 3R_20770426_SNP [dm6]	G	T	2.755e^-5	0.591	DOWNSTREAM Takl1 INTRON Syp	TF binding site mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_HSA
2R	10542085	2R_10542085_SNP [dm3] 2R_14654580_SNP [dm6]	C	G	2.766e^-5	0.591	INTERGENIC
3R	20396578	3R_20396578_SNP [dm3] 3R_24570856_SNP [dm6]	G	T	2.792e^-5	0.591	INTRON CG13624
2L	15176639	2L_15176639_SNP [dm3] 2L_15176639_SNP [dm6]	G	A	2.899e^-5	0.591	INTRON CG4168
3R	22696118	3R_22696118_SNP [dm3] 3R_26870396_SNP [dm6]	T	C	2.919e^-5	0.591	INTRON BM-40-SPARC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	12721530	2L_12721530_SNP [dm3] 2L_12721530_SNP [dm6]	A	G	2.940e^-5	0.591	SYNONYMOUS_CODING CG5792 UPSTREAM MRP INTRON MRP	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	18971433	3R_18971433_SNP [dm3] 3R_23145711_SNP [dm6]	T	C	2.978e^-5	0.591	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E
2L	16543887	2L_16543887_SNP [dm3] 2L_16543887_SNP [dm6]	C	A	2.986e^-5	0.591	DOWNSTREAM CG31816 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2L	12727225	2L_12727225_SNP [dm3] 2L_12727225_SNP [dm6]	T	G	3.007e^-5	0.591	INTRON MRP
3L	12630150	3L_12630150_SNP [dm3] 3L_12637050_SNP [dm6]	A	C	3.084e^-5	0.591	INTRON CR32111
2L	12724589	2L_12724589_SNP [dm3] 2L_12724589_SNP [dm6]	C	T	3.195e^-5	0.591	SYNONYMOUS_CODING MRP INTRON MRP	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	19572941	2L_19572941_SNP [dm3] 2L_19572941_SNP [dm6]	C	G	3.321e^-5	0.591	UPSTREAM spi INTRON spi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
3R	23475233	3R_23475233_SNP [dm3] 3R_27649511_SNP [dm6]	C	T	3.345e^-5	0.591	UTR_5_PRIME tau INTRON tau
2L	9181030	2L_9181030_SNP [dm3] 2L_9181030_SNP [dm6]	C	T	3.379e^-5	0.591	INTRON tai
3L	2717613	3L_2717613_SNP [dm3] 3L_2717613_SNP [dm6]	T	C	3.404e^-5	0.591	DOWNSTREAM Mrtf INTERGENIC
2R	14218931	2R_14218931_SNP [dm3] 2R_18331426_SNP [dm6]	G	A	3.413e^-5	0.591	INTRON sbb
X	11098538	X_11098538_DEL [dm3] X_11204505_DEL [dm6]	TT	T	3.429e^-5	0.591	INTERGENIC
X	3270711	X_3270711_SNP [dm3] X_3376678_SNP [dm6]	A	C	3.444e^-5	0.591	INTRON dm & 1 other
3R	13765205	3R_13765205_SNP [dm3] 3R_17939483_SNP [dm6]	C	T	3.510e^-5	0.591	INTRON cpo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13765207	3R_13765207_SNP [dm3] 3R_17939485_SNP [dm6]	A	G	3.510e^-5	0.591	INTRON cpo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	14282612	2L_14282612_SNP [dm3] 2L_14282612_SNP [dm6]	C	T	3.543e^-5	0.591	INTRON wb
2R	10932478	2R_10932478_SNP [dm3] 2R_15044973_SNP [dm6]	G	C	3.567e^-5	0.591	INTERGENIC
2R	10542130	2R_10542130_DEL [dm3] 2R_14654625_DEL [dm6]	CCAACAC	TG	3.623e^-5	0.591	INTERGENIC
2L	14277924	2L_14277924_SNP [dm3] 2L_14277924_SNP [dm6]	A	T	3.646e^-5	0.591	UTR_3_PRIME CG32971 INTRON wb
X	11072409	X_11072409_SNP [dm3] X_11178376_SNP [dm6]	T	A	3.747e^-5	0.591	INTERGENIC
2R	10542141	2R_10542141_DEL [dm3] 2R_14654636_DEL [dm6]	AATGCAAAACACAAAGA...	A	3.790e^-5	0.591	INTERGENIC
3R	26169789	3R_26169789_SNP [dm3] 3R_30344067_SNP [dm6]	A	T	3.829e^-5	0.591	INTRON hdc	TF binding site BDTNP1_TFBS_dl
2R	11883363	2R_11883363_SNP [dm3] 2R_15995858_SNP [dm6]	A	G	3.862e^-5	0.591	SYNONYMOUS_CODING ATPCL
3R	22696155	3R_22696155_SNP [dm3] 3R_26870433_SNP [dm6]	T	A	3.995e^-5	0.591	INTRON BM-40-SPARC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3R	25145604	3R_25145604_SNP [dm3] 3R_29319882_SNP [dm6]	A	C	4.016e^-5	0.591	UPSTREAM Cnx99A INTERGENIC
X	11072233	X_11072233_SNP [dm3] X_11178200_SNP [dm6]	G	T	4.100e^-5	0.591	INTERGENIC
2L	6702311	2L_6702311_SNP [dm3] 2L_6702311_SNP [dm6]	G	A	4.145e^-5	0.591	INTRON Tsp
2R	10544454	2R_10544454_SNP [dm3] 2R_14656949_SNP [dm6]	T	C	4.148e^-5	0.591	NON_SYNONYMOUS_CODING Adgf-E

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By genomic position
Variant impact
Gene name

Cuticul_2_Me_C22 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