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=3.409e^-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

Covariate	p-value	Significance
In_2L_t	0.02384

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.1206	0.0469

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2213 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
3L	415143	3L_415143_DEL [dm3] 3L_415143_DEL [dm6]	AA	A	4.777e^-7	0.826	INTERGENIC
X	20262267	X_20262267_SNP [dm3] X_20391240_SNP [dm6]	A	G	1.428e^-6	0.826	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	20272005	X_20272005_SNP [dm3] X_20400978_SNP [dm6]	A	T	2.639e^-6	0.826	SYNONYMOUS_CODING HERC2	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	5963561	3R_5963561_SNP [dm3] 3R_10137839_SNP [dm6]	T	C	3.198e^-6	0.826	INTRON tws	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	412023	3L_412023_SNP [dm3] 3L_412023_SNP [dm6]	G	T	4.150e^-6	0.826	INTERGENIC
3L	413912	3L_413912_SNP [dm3] 3L_413912_SNP [dm6]	C	T	4.245e^-6	0.826	INTERGENIC	TF binding site mE1_TFBS_Kr
2R	12116819	2R_12116819_SNP [dm3] 2R_16229314_SNP [dm6]	A	G	4.384e^-6	0.826	SYNONYMOUS_CODING Tsf3 UPSTREAM CG15701 INTRON CG15706	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	15844015	2R_15844015_SNP [dm3] 2R_19956510_SNP [dm6]	A	C	5.595e^-6	0.826	SYNONYMOUS_CODING CG44623
2L	5511194	2L_5511194_SNP [dm3] 2L_5511194_SNP [dm6]	A	C	5.781e^-6	0.826	INTERGENIC
2R	11813555	2R_11813555_SNP [dm3] 2R_15926050_SNP [dm6]	G	A	5.892e^-6	0.826	SYNONYMOUS_CODING bdg	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	16407833	2R_16407833_SNP [dm3] 2R_20520328_SNP [dm6]	G	A	6.240e^-6	0.826	INTERGENIC
2R	12116981	2R_12116981_SNP [dm3] 2R_16229476_SNP [dm6]	C	T	7.177e^-6	0.826	SYNONYMOUS_CODING Tsf3 UPSTREAM CG15701 INTRON CG15706	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	7.462e^-6	0.826	INTERGENIC
3L	14815465	3L_14815465_SNP [dm3] 3L_14822365_SNP [dm6]	G	A	7.655e^-6	0.826	INTRON CG17839
X	20262270	X_20262270_INS [dm3] X_20391243_INS [dm6]	A	ATCAATAATAATTCAA...	8.445e^-6	0.826	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13505970	2R_13505970_SNP [dm3] 2R_17618465_SNP [dm6]	C	A	8.632e^-6	0.826	UPSTREAM CG44403 INTRON CG10936
3L	413923	3L_413923_SNP [dm3] 3L_413923_SNP [dm6]	A	G	8.668e^-6	0.826	INTERGENIC	TF binding site mE1_TFBS_Kr
2L	3298739	2L_3298739_SNP [dm3] 2L_3298739_SNP [dm6]	T	C	8.807e^-6	0.826	INTRON CG9663	TF binding site BDTNP1_TFBS_da
2R	11648030	2R_11648030_SNP [dm3] 2R_15760525_SNP [dm6]	A	T	9.525e^-6	0.826	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11813744	2R_11813744_SNP [dm3] 2R_15926239_SNP [dm6]	C	T	1.046e^-5	0.826	SYNONYMOUS_CODING bdg	TF binding site mE1_TFBS_cad
3L	16896011	3L_16896011_SNP [dm3] 3L_16902911_SNP [dm6]	A	T	1.078e^-5	0.826	NON_SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_chinmo
X	20262315	X_20262315_DEL [dm3] X_20391288_DEL [dm6]	TGATGTTTCTTAT...	T	1.135e^-5	0.826	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8404903	X_8404903_DEL [dm3] X_8510870_DEL [dm6]	ATTA	A	1.268e^-5	0.826	INTRON CG33181	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15428091	2R_15428091_SNP [dm3] 2R_19540586_SNP [dm6]	C	A	1.322e^-5	0.826	INTRON sm
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	1.364e^-5	0.826	INTERGENIC
3L	4152861	3L_4152861_SNP [dm3] 3L_4152861_SNP [dm6]	G	A	1.451e^-5	0.826	DOWNSTREAM CG1299 & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6899768	3L_6899768_SNP [dm3] 3L_6906668_SNP [dm6]	A	T	1.465e^-5	0.826	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	10581745	2R_10581745_SNP [dm3] 2R_14694240_SNP [dm6]	A	G	1.506e^-5	0.826	INTRON mspo
2R	15884106	2R_15884106_SNP [dm3] 2R_19996601_SNP [dm6]	G	C	1.662e^-5	0.826	INTERGENIC
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	1.667e^-5	0.826	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10691485	3L_10691485_SNP [dm3] 3L_10698385_SNP [dm6]	T	G	1.667e^-5	0.826	INTERGENIC
3L	8207850	3L_8207850_SNP [dm3] 3L_8214750_SNP [dm6]	T	C	1.724e^-5	0.826	UPSTREAM CG8012 INTERGENIC
3R	4362491	3R_4362491_SNP [dm3] 3R_8536769_SNP [dm6]	A	G	1.796e^-5	0.826	INTERGENIC
3R	4331834	3R_4331834_SNP [dm3] 3R_8506112_SNP [dm6]	C	T	1.809e^-5	0.826	INTERGENIC	TF binding site mE1_TFBS_cad
X	1931082	X_1931082_SNP [dm3] X_2037049_SNP [dm6]	A	G	1.983e^-5	0.826	UPSTREAM Actn INTRON Actn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	4841144	3L_4841144_SNP [dm3] 3L_4841144_SNP [dm6]	C	T	2.043e^-5	0.826	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2R	18962423	2R_18962423_SNP [dm3] 2R_23074900_SNP [dm6]	C	T	2.129e^-5	0.826	UTR_5_PRIME CG3085 UPSTREAM snoRNA:229 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12159601	3L_12159601_SNP [dm3] 3L_12166501_SNP [dm6]	T	C	2.202e^-5	0.826	SYNONYMOUS_CODING Rh7	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4696998	3L_4696998_SNP [dm3] 3L_4696998_SNP [dm6]	G	T	2.224e^-5	0.826	UPSTREAM CG13713 INTRON RhoGEF64C	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	4697013	3L_4697013_SNP [dm3] 3L_4697013_SNP [dm6]	G	A	2.224e^-5	0.826	UPSTREAM CG13713 INTRON RhoGEF64C	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	13139061	3R_13139061_SNP [dm3] 3R_17313339_SNP [dm6]	G	T	2.257e^-5	0.826	INTERGENIC
3R	13175133	3R_13175133_SNP [dm3] 3R_17349411_SNP [dm6]	A	C	2.271e^-5	0.826	INTRON beat-IIa
3R	5087274	3R_5087274_SNP [dm3] 3R_9261552_SNP [dm6]	C	A	2.295e^-5	0.826	INTRON VhaM8.9	TF binding site mE1_TFBS_HSA
3L	1010439	3L_1010439_SNP [dm3] 3L_1010439_SNP [dm6]	A	G	2.379e^-5	0.826	INTRON trio
2L	8929077	2L_8929077_SNP [dm3] 2L_8929077_SNP [dm6]	A	G	2.444e^-5	0.826	NON_SYNONYMOUS_CODING CG34398	TF binding site mE1_TFBS_cad
3L	14565106	3L_14565106_DEL [dm3] 3L_14572006_DEL [dm6]	TT	T	2.509e^-5	0.826	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	8556612	3L_8556612_SNP [dm3] 3L_8563512_SNP [dm6]	C	G	2.582e^-5	0.826	INTRON rhea
2L	19522029	2L_19522029_SNP [dm3] 2L_19522029_SNP [dm6]	C	T	2.633e^-5	0.826	SYNONYMOUS_CODING CG10132	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1381522	2L_1381522_SNP [dm3] 2L_1381522_SNP [dm6]	T	C	2.640e^-5	0.826	SYNONYMOUS_CODING lea UTR_3_PRIME lea UPSTREAM CR44898 EXON CR44897	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3L	6600205	3L_6600205_SNP [dm3] 3L_6607105_SNP [dm6]	T	G	2.658e^-5	0.826	INTRON CG8368	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	8388326	3R_8388326_SNP [dm3] 3R_12562604_SNP [dm6]	C	T	2.738e^-5	0.826	UTR_5_PRIME Octbeta2R INTRON Octbeta2R
3R	14623691	3R_14623691_INS [dm3] 3R_18797969_INS [dm6]	T	TGT	2.776e^-5	0.826	INTERGENIC
2L	16239804	2L_16239804_SNP [dm3] 2L_16239804_SNP [dm6]	C	T	2.793e^-5	0.826	INTRON CG42817
2R	11823073	2R_11823073_SNP [dm3] 2R_15935568_SNP [dm6]	A	C	2.889e^-5	0.826	NON_SYNONYMOUS_CODING CG8297 UPSTREAM Iap2 DOWNSTREAM Mlf	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	15843970	2R_15843970_SNP [dm3] 2R_19956465_SNP [dm6]	C	T	2.923e^-5	0.826	SYNONYMOUS_CODING CG44623
2R	13506075	2R_13506075_SNP [dm3] 2R_17618570_SNP [dm6]	T	G	2.935e^-5	0.826	UPSTREAM CG44403 INTRON CG10936
2R	11647915	2R_11647915_SNP [dm3] 2R_15760410_SNP [dm6]	G	A	2.949e^-5	0.826	INTRON CG30089	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7700782	2L_7700782_SNP [dm3] 2L_7700782_SNP [dm6]	T	C	2.954e^-5	0.826	INTRON Tep2
X	8173885	X_8173885_SNP [dm3] X_8279852_SNP [dm6]	C	A	3.004e^-5	0.826	UTR_3_PRIME nAChRalpha3	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu
2L	19079203	2L_19079203_SNP [dm3] 2L_19079203_SNP [dm6]	C	T	3.074e^-5	0.826	UPSTREAM CG10700 DOWNSTREAM Lim3 INTERGENIC
3L	14710885	3L_14710885_DEL [dm3] 3L_14717785_DEL [dm6]	GAAAAA	T	3.111e^-5	0.826	INTRON ome
2L	22020494	2L_22020494_SNP [dm3] 2L_22020494_SNP [dm6]	A	G	3.148e^-5	0.826	DOWNSTREAM CR33987 INTRON tio	TF binding site mE1_TFBS_Trl
2L	19808957	2L_19808957_SNP [dm3] 2L_19808957_SNP [dm6]	T	A	3.221e^-5	0.826	INTRON sick	TF binding site mE1_TFBS_cad
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	3.436e^-5	0.826	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	19079217	2L_19079217_SNP [dm3] 2L_19079217_SNP [dm6]	A	T	3.474e^-5	0.826	UPSTREAM CG10700 DOWNSTREAM Lim3 INTERGENIC
3R	8390929	3R_8390929_SNP [dm3] 3R_12565207_SNP [dm6]	T	C	3.479e^-5	0.826	INTRON Octbeta2R
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	3.508e^-5	0.826	INTRON CG17839
2R	15843992	2R_15843992_SNP [dm3] 2R_19956487_SNP [dm6]	G	T	3.513e^-5	0.826	NON_SYNONYMOUS_CODING CG44623
2R	15884102	2R_15884102_SNP [dm3] 2R_19996597_SNP [dm6]	T	G	3.562e^-5	0.826	INTERGENIC
3L	15581190	3L_15581190_SNP [dm3] 3L_15588090_SNP [dm6]	C	A	3.765e^-5	0.826	UTR_5_PRIME CG7656 UPSTREAM RhoGAP71E & 1 other	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_shn mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
X	8402895	X_8402895_DEL [dm3] X_8508862_DEL [dm6]	TGCG	T	3.769e^-5	0.826	UPSTREAM CG33181 INTRON CG33181
3R	6048371	3R_6048371_SNP [dm3] 3R_10222649_SNP [dm6]	C	T	3.776e^-5	0.826	UPSTREAM CG12420 DOWNSTREAM CG12817 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	8507658	2L_8507658_SNP [dm3] 2L_8507658_SNP [dm6]	G	C	3.892e^-5	0.826	UPSTREAM Dh31 INTERGENIC
3R	22435414	3R_22435414_SNP [dm3] 3R_26609692_SNP [dm6]	G	T	3.971e^-5	0.826	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	11809705	2R_11809705_SNP [dm3] 2R_15922200_SNP [dm6]	G	A	3.982e^-5	0.826	UPSTREAM sli DOWNSTREAM bdg INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_bab1 mE1_TFBS_HSA
2L	6581643	2L_6581643_SNP [dm3] 2L_6581643_SNP [dm6]	A	T	4.026e^-5	0.826	INTRON CG11319
2L	11686615	2L_11686615_SNP [dm3] 2L_11686615_SNP [dm6]	A	G	4.037e^-5	0.826	INTERGENIC
2R	15844033	2R_15844033_SNP [dm3] 2R_19956528_SNP [dm6]	T	G	4.082e^-5	0.826	SYNONYMOUS_CODING CG44623
2L	11686657	2L_11686657_SNP [dm3] 2L_11686657_SNP [dm6]	T	C	4.168e^-5	0.826	INTERGENIC
3R	3975957	3R_3975957_SNP [dm3] 3R_8150235_SNP [dm6]	T	C	4.177e^-5	0.826	INTRON grn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3R	3469607	3R_3469607_SNP [dm3] 3R_7643885_SNP [dm6]	C	T	4.347e^-5	0.826	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	8507679	2L_8507679_SNP [dm3] 2L_8507679_SNP [dm6]	T	A	4.354e^-5	0.826	UPSTREAM Dh31 INTERGENIC
2L	11686606	2L_11686606_SNP [dm3] 2L_11686606_SNP [dm6]	A	T	4.410e^-5	0.826	INTERGENIC
2L	8507668	2L_8507668_SNP [dm3] 2L_8507668_SNP [dm6]	G	C	4.505e^-5	0.826	UPSTREAM Dh31 INTERGENIC
3R	17931811	3R_17931811_SNP [dm3] 3R_22106089_SNP [dm6]	T	C	4.510e^-5	0.826	DOWNSTREAM CG13407 INTRON CG5778
3L	8582894	3L_8582894_SNP [dm3] 3L_8589794_SNP [dm6]	G	C	4.563e^-5	0.826	UPSTREAM CG43078 INTRON CG43078
X	8678910	X_8678910_SNP [dm3] X_8784877_SNP [dm6]	G	A	4.578e^-5	0.826	INTRON Lim1
X	8678911	X_8678911_SNP [dm3] X_8784878_SNP [dm6]	C	A	4.578e^-5	0.826	INTRON Lim1
X	8678929	X_8678929_SNP [dm3] X_8784896_SNP [dm6]	A	C	4.578e^-5	0.826	INTRON Lim1
3R	8274107	3R_8274107_SNP [dm3] 3R_12448385_SNP [dm6]	G	A	4.593e^-5	0.826	NON_SYNONYMOUS_CODING CG5538 UPSTREAM CG18549 DOWNSTREAM Desat1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	2935012	2R_2935012_SNP [dm3] 2R_7047507_SNP [dm6]	T	A	4.626e^-5	0.826	NON_SYNONYMOUS_CODING Tsp42El
2L	11686609	2L_11686609_SNP [dm3] 2L_11686609_SNP [dm6]	G	A	4.643e^-5	0.826	INTERGENIC
3L	14388889	3L_14388889_SNP [dm3] 3L_14395789_SNP [dm6]	G	A	5.027e^-5	0.826	INTERGENIC
X	20215452	X_20215452_INS [dm3] X_20344425_INS [dm6]	AC	TTATGCCG	5.136e^-5	0.826	INTERGENIC
X	3154188	X_3154188_SNP [dm3] X_3260155_SNP [dm6]	C	T	5.137e^-5	0.826	INTRON dnc
3L	15728431	3L_15728431_SNP [dm3] 3L_15735331_SNP [dm6]	A	G	5.157e^-5	0.826	INTERGENIC
X	8678952	X_8678952_SNP [dm3] X_8784919_SNP [dm6]	T	C	5.164e^-5	0.826	INTRON Lim1
2L	3417494	2L_3417494_SNP [dm3] 2L_3417494_SNP [dm6]	A	T	5.234e^-5	0.826	UTR_3_PRIME CG31952 INTRON pgant2
2L	11686631	2L_11686631_DEL [dm3] 2L_11686631_DEL [dm6]	ATTACAGGTAATA...	T	5.255e^-5	0.826	INTERGENIC
3L	412168	3L_412168_SNP [dm3] 3L_412168_SNP [dm6]	G	A	5.292e^-5	0.826	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=3.562e^-2)
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	0.04488

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.6654	0.0357

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2076 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	1.827e^-6	0.889	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	2.609e^-6	0.889	INTERGENIC
3L	14815037	3L_14815037_SNP [dm3] 3L_14821937_SNP [dm6]	A	C	5.823e^-6	0.889	INTRON CG17839
3L	14815465	3L_14815465_SNP [dm3] 3L_14822365_SNP [dm6]	G	A	6.106e^-6	0.889	INTRON CG17839
3L	14817336	3L_14817336_SNP [dm3] 3L_14824236_SNP [dm6]	G	A	6.279e^-6	0.889	INTRON CG17839
3L	14817946	3L_14817946_SNP [dm3] 3L_14824846_SNP [dm6]	A	G	6.480e^-6	0.889	INTRON CG17839
3L	14813879	3L_14813879_SNP [dm3] 3L_14820779_SNP [dm6]	A	T	7.424e^-6	0.889	INTRON CG17839
3L	14813565	3L_14813565_SNP [dm3] 3L_14820465_SNP [dm6]	G	A	9.561e^-6	0.889	INTRON CG17839
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	1.036e^-5	0.889	INTRON CG17839
2R	14086288	2R_14086288_SNP [dm3] 2R_18198783_SNP [dm6]	A	C	1.061e^-5	0.889	INTERGENIC
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	1.064e^-5	0.889	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	15559759	X_15559759_SNP [dm3] X_15665726_SNP [dm6]	A	G	1.101e^-5	0.889	UPSTREAM CR43299 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	14817116	3L_14817116_SNP [dm3] 3L_14824016_SNP [dm6]	A	T	1.107e^-5	0.889	INTRON CG17839
3R	13570329	3R_13570329_SNP [dm3] 3R_17744607_SNP [dm6]	A	C	1.194e^-5	0.889	INTRON TyrRII	TF binding site mE1_TFBS_cad
2L	1931534	2L_1931534_SNP [dm3] 2L_1931534_SNP [dm6]	A	G	1.207e^-5	0.889	INTRON CG7337
3L	2644859	3L_2644859_SNP [dm3] 3L_2644859_SNP [dm6]	C	T	1.243e^-5	0.889	UPSTREAM CG1143 INTERGENIC
3R	20851748	3R_20851748_SNP [dm3] 3R_25026026_SNP [dm6]	G	A	1.276e^-5	0.889	SYNONYMOUS_CODING Hr96	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna
3R	13175133	3R_13175133_SNP [dm3] 3R_17349411_SNP [dm6]	A	C	1.330e^-5	0.889	INTRON beat-IIa
3R	4331834	3R_4331834_SNP [dm3] 3R_8506112_SNP [dm6]	C	T	1.339e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_cad
3L	14813646	3L_14813646_SNP [dm3] 3L_14820546_SNP [dm6]	G	A	1.344e^-5	0.889	INTRON CG17839
3L	14828782	3L_14828782_SNP [dm3] 3L_14835682_SNP [dm6]	A	C	1.642e^-5	0.889	INTRON CG17839
2L	11686657	2L_11686657_SNP [dm3] 2L_11686657_SNP [dm6]	T	C	1.792e^-5	0.889	INTERGENIC
3L	18359255	3L_18359255_SNP [dm3] 3L_18366155_SNP [dm6]	A	C	1.912e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_cad
2R	15844015	2R_15844015_SNP [dm3] 2R_19956510_SNP [dm6]	A	C	1.925e^-5	0.889	SYNONYMOUS_CODING CG44623
2R	11648030	2R_11648030_SNP [dm3] 2R_15760525_SNP [dm6]	A	T	1.972e^-5	0.889	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	2.001e^-5	0.889	INTERGENIC
3R	9916835	3R_9916835_SNP [dm3] 3R_14091113_SNP [dm6]	C	T	2.057e^-5	0.889	INTRON Npc2b
3L	19448906	3L_19448906_SNP [dm3] 3L_19455806_SNP [dm6]	A	G	2.058e^-5	0.889	DOWNSTREAM CR45434 INTERGENIC
3L	14811233	3L_14811233_SNP [dm3] 3L_14818133_SNP [dm6]	C	T	2.183e^-5	0.889	INTRON CG17839
2L	19737343	2L_19737343_SNP [dm3] 2L_19737343_SNP [dm6]	G	T	2.225e^-5	0.889	DOWNSTREAM Nf-YB INTERGENIC
3L	10694223	3L_10694223_SNP [dm3] 3L_10701123_SNP [dm6]	C	A	2.407e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	13238252	2R_13238252_SNP [dm3] 2R_17350747_SNP [dm6]	A	C	2.478e^-5	0.889	INTRON mbl
3L	10694245	3L_10694245_SNP [dm3] 3L_10701145_SNP [dm6]	G	A	2.508e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	9873427	3L_9873427_SNP [dm3] 3L_9880327_SNP [dm6]	A	G	2.618e^-5	0.889	SYNONYMOUS_CODING CG34382	TF binding site mE1_TFBS_chinmo
X	2926734	X_2926734_SNP [dm3] X_3032701_SNP [dm6]	C	A	2.619e^-5	0.889	INTRON kirre
2L	15084985	2L_15084985_SNP [dm3] 2L_15084985_SNP [dm6]	A	T	2.627e^-5	0.889	INTRON CG15270
2R	11576600	2R_11576600_SNP [dm3] 2R_15689095_SNP [dm6]	G	T	2.689e^-5	0.889	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	2926031	X_2926031_SNP [dm3] X_3031998_SNP [dm6]	C	A	2.693e^-5	0.889	INTRON kirre
3L	14813812	3L_14813812_SNP [dm3] 3L_14820712_SNP [dm6]	C	A	2.734e^-5	0.889	INTRON CG17839
2R	11576437	2R_11576437_SNP [dm3] 2R_15688932_SNP [dm6]	T	C	2.817e^-5	0.889	NON_SYNONYMOUS_CODING Cep89 UPSTREAM CG30090	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3L	14814974	3L_14814974_SNP [dm3] 3L_14821874_SNP [dm6]	A	G	2.823e^-5	0.889	INTRON CG17839
2R	12520352	2R_12520352_SNP [dm3] 2R_16632847_SNP [dm6]	G	T	2.988e^-5	0.889	SYNONYMOUS_CODING Alk	TF binding site mE1_TFBS_cad
2R	18278806	2R_18278806_SNP [dm3] 2R_22391301_SNP [dm6]	A	G	2.992e^-5	0.889	SYNONYMOUS_CODING CG13506	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	11647915	2R_11647915_SNP [dm3] 2R_15760410_SNP [dm6]	G	A	3.051e^-5	0.889	INTRON CG30089	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12896052	2L_12896052_SNP [dm3] 2L_12896052_SNP [dm6]	T	C	3.058e^-5	0.889	INTERGENIC
2R	12696827	2R_12696827_SNP [dm3] 2R_16809322_SNP [dm6]	C	A	3.149e^-5	0.889	INTERGENIC
3R	13469273	3R_13469273_SNP [dm3] 3R_17643551_SNP [dm6]	T	C	3.227e^-5	0.889	INTRON CG43175
X	8678837	X_8678837_SNP [dm3] X_8784804_SNP [dm6]	C	T	3.247e^-5	0.889	INTRON Lim1
3L	12446661	3L_12446661_SNP [dm3] 3L_12453561_SNP [dm6]	A	G	3.269e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_Kr
3R	15047041	3R_15047041_DEL [dm3] 3R_19221319_DEL [dm6]	CACATAATAC	C	3.291e^-5	0.889	INTRON vib	TF binding site mE1_TFBS_inv
X	8402577	X_8402577_SNP [dm3] X_8508544_SNP [dm6]	G	A	3.336e^-5	0.889	INTRON CG33181
3L	14057292	3L_14057292_SNP [dm3] 3L_14064192_SNP [dm6]	C	T	3.425e^-5	0.889	INTRON CG32138	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	15843970	2R_15843970_SNP [dm3] 2R_19956465_SNP [dm6]	C	T	3.437e^-5	0.889	SYNONYMOUS_CODING CG44623
3L	19472074	3L_19472074_SNP [dm3] 3L_19478974_SNP [dm6]	G	A	3.473e^-5	0.889	UPSTREAM CR32207 DOWNSTREAM CR42842 INTERGENIC
2L	7057433	2L_7057433_SNP [dm3] 2L_7057433_SNP [dm6]	C	T	3.553e^-5	0.889	SYNONYMOUS_CODING Mnn1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	20936762	X_20936762_SNP [dm3] X_21065735_SNP [dm6]	G	A	3.684e^-5	0.889	INTRON bves & 1 other
3L	3680402	3L_3680402_SNP [dm3] 3L_3680402_SNP [dm6]	T	C	3.692e^-5	0.889	INTERGENIC
3L	14827010	3L_14827010_SNP [dm3] 3L_14833910_SNP [dm6]	G	T	3.799e^-5	0.889	INTRON CG17839
X	8404903	X_8404903_DEL [dm3] X_8510870_DEL [dm6]	ATTA	A	3.841e^-5	0.889	INTRON CG33181	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11686646	2L_11686646_SNP [dm3] 2L_11686646_SNP [dm6]	A	T	3.961e^-5	0.889	INTERGENIC
3L	4164481	3L_4164481_SNP [dm3] 3L_4164481_SNP [dm6]	A	T	4.060e^-5	0.889	SYNONYMOUS_CODING mas	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	12030323	2L_12030323_SNP [dm3] 2L_12030323_SNP [dm6]	C	A	4.107e^-5	0.889	INTRON dmGlut	TF binding site mE1_TFBS_cad
3L	10197266	3L_10197266_SNP [dm3] 3L_10204166_SNP [dm6]	A	G	4.108e^-5	0.889	INTERGENIC
3L	10691485	3L_10691485_SNP [dm3] 3L_10698385_SNP [dm6]	T	G	4.141e^-5	0.889	INTERGENIC
X	1931082	X_1931082_SNP [dm3] X_2037049_SNP [dm6]	A	G	4.173e^-5	0.889	UPSTREAM Actn INTRON Actn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	13139061	3R_13139061_SNP [dm3] 3R_17313339_SNP [dm6]	G	T	4.250e^-5	0.889	INTERGENIC
2R	14620448	2R_14620448_SNP [dm3] 2R_18732943_SNP [dm6]	T	A	4.349e^-5	0.889	INTRON Hs3st-A
2R	15843992	2R_15843992_SNP [dm3] 2R_19956487_SNP [dm6]	G	T	4.358e^-5	0.889	NON_SYNONYMOUS_CODING CG44623
3L	12446783	3L_12446783_SNP [dm3] 3L_12453683_SNP [dm6]	C	A	4.378e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_Kr
2R	13772991	2R_13772991_SNP [dm3] 2R_17885486_SNP [dm6]	C	T	4.382e^-5	0.889	INTRON Elk
2L	12527947	2L_12527947_SNP [dm3] 2L_12527947_SNP [dm6]	C	T	4.387e^-5	0.889	INTRON bun	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	15844090	2R_15844090_SNP [dm3] 2R_19956585_SNP [dm6]	T	A	4.416e^-5	0.889	SPLICE_SITE_REGION CG44623 INTRON CG44623
3L	2644981	3L_2644981_SNP [dm3] 3L_2644981_SNP [dm6]	A	T	4.520e^-5	0.889	UPSTREAM CG1143 INTERGENIC
3L	8745109	3L_8745109_SNP [dm3] 3L_8752009_SNP [dm6]	A	G	4.742e^-5	0.889	UPSTREAM CR44527 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	21600286	3L_21600286_INS [dm3] 3L_21607186_INS [dm6]	C	CACCTATGTTC...	4.750e^-5	0.889	UPSTREAM TfAP-2 INTRON TfAP-2
2R	11582501	2R_11582501_SNP [dm3] 2R_15694996_SNP [dm6]	G	C	4.840e^-5	0.889	SYNONYMOUS_CODING CG33460 UPSTREAM CG33461
3L	12446726	3L_12446726_SNP [dm3] 3L_12453626_SNP [dm6]	A	C	4.842e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_Kr
3R	8409015	3R_8409015_SNP [dm3] 3R_12583293_SNP [dm6]	T	G	4.860e^-5	0.889	INTRON Octbeta2R
3L	781261	3L_781261_SNP [dm3] 3L_781261_SNP [dm6]	G	T	4.932e^-5	0.889	INTERGENIC
X	18730960	X_18730960_SNP [dm3] X_18836927_SNP [dm6]	A	T	4.971e^-5	0.889	INTRON Pvf1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	4950454	2R_4950454_SNP [dm3] 2R_9062949_SNP [dm6]	G	A	5.056e^-5	0.889	INTRON ana	regulatory region REDfly_CRMs
X	5603582	X_5603582_SNP [dm3] X_5709549_SNP [dm6]	G	A	5.065e^-5	0.889	SYNONYMOUS_CODING CG33080 DOWNSTREAM CG4096	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3R	4938644	3R_4938644_SNP [dm3] 3R_9112922_SNP [dm6]	C	A	5.155e^-5	0.889	INTRON pum
3L	14816333	3L_14816333_SNP [dm3] 3L_14823233_SNP [dm6]	G	A	5.190e^-5	0.889	INTRON CG17839
X	16098245	X_16098245_SNP [dm3] X_16204212_SNP [dm6]	G	C	5.193e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr
3L	16983394	3L_16983394_SNP [dm3] 3L_16990294_SNP [dm6]	C	A	5.226e^-5	0.889	INTRON Exn
2R	14620466	2R_14620466_SNP [dm3] 2R_18732961_SNP [dm6]	C	T	5.227e^-5	0.889	INTRON Hs3st-A
2L	11686631	2L_11686631_DEL [dm3] 2L_11686631_DEL [dm6]	ATTACAGGTAATA...	T	5.302e^-5	0.889	INTERGENIC
2R	13237688	2R_13237688_SNP [dm3] 2R_17350183_SNP [dm6]	T	C	5.362e^-5	0.889	INTRON mbl
2L	7451999	2L_7451999_SNP [dm3] 2L_7451999_SNP [dm6]	G	A	5.415e^-5	0.889	UPSTREAM santa-maria DOWNSTREAM Gr28a INTERGENIC	TF binding site BDTNP1_TFBS_ftz mE1_TFBS_HSA
2L	11686615	2L_11686615_SNP [dm3] 2L_11686615_SNP [dm6]	A	G	5.419e^-5	0.889	INTERGENIC
X	19871890	X_19871890_SNP [dm3] X_19977857_SNP [dm6]	C	T	5.445e^-5	0.889	INTERGENIC
3R	4341488	3R_4341488_SNP [dm3] 3R_8515766_SNP [dm6]	G	A	5.458e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	5087274	3R_5087274_SNP [dm3] 3R_9261552_SNP [dm6]	C	A	5.537e^-5	0.889	INTRON VhaM8.9	TF binding site mE1_TFBS_HSA
2R	12116819	2R_12116819_SNP [dm3] 2R_16229314_SNP [dm6]	A	G	5.561e^-5	0.889	SYNONYMOUS_CODING Tsf3 UPSTREAM CG15701 INTRON CG15706	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	10694292	3L_10694292_SNP [dm3] 3L_10701192_SNP [dm6]	G	C	5.585e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	4346178	3R_4346178_SNP [dm3] 3R_8520456_SNP [dm6]	T	C	5.628e^-5	0.889	SYNONYMOUS_CODING CG11737	TF binding site mE1_TFBS_chinmo
3L	3835090	3L_3835090_INS [dm3] 3L_3835090_INS [dm6]	A	AATATAACTATC...	5.668e^-5	0.889	INTRON enc
3L	781279	3L_781279_SNP [dm3] 3L_781279_SNP [dm6]	G	A	5.699e^-5	0.889	INTERGENIC
2L	19802421	2L_19802421_SNP [dm3] 2L_19802421_SNP [dm6]	A	C	5.755e^-5	0.889	INTRON sick

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By genomic position
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Gene name

Wing_Intervein_Area1 phenotype

Phenotype distribution and association to known covariates

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GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results