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=1.785e^-3)
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_3R_K	0.07665

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2150 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
2R	9679611	2R_9679611_DEL [dm3] 2R_13792106_DEL [dm6]	CC	C	2.962e^-7	0.556	EXON CR43811
2R	14676098	2R_14676098_SNP [dm3] 2R_18788593_SNP [dm6]	C	T	2.214e^-6	0.808	INTRON CG15080
2R	19573478	2R_19573478_SNP [dm3] 2R_23685955_SNP [dm6]	C	T	2.323e^-6	0.808	UPSTREAM l_2_efl INTRON St3
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	2.546e^-6	0.808	INTRON Spn
2R	9676496	2R_9676496_SNP [dm3] 2R_13788991_SNP [dm6]	T	C	3.046e^-6	0.808	INTERGENIC
2R	8114508	2R_8114508_SNP [dm3] 2R_12227003_SNP [dm6]	C	T	3.217e^-6	0.808	UPSTREAM CG8854 INTRON CG8854
2R	1352419	2R_1352419_SNP [dm3] 2R_5464914_SNP [dm6]	G	T	4.360e^-6	0.808	INTERGENIC	transposable element FlyBase
2R	1354359	2R_1354359_SNP [dm3] 2R_5466854_SNP [dm6]	C	A	4.955e^-6	0.808	INTERGENIC	transposable element FlyBase
X	16925265	X_16925265_SNP [dm3] X_17031232_SNP [dm6]	G	C	4.993e^-6	0.808	INTRON CG45002
2R	1354357	2R_1354357_SNP [dm3] 2R_5466852_SNP [dm6]	G	T	5.847e^-6	0.808	INTERGENIC	transposable element FlyBase
2R	17647628	2R_17647628_SNP [dm3] 2R_21760123_SNP [dm6]	C	A	6.268e^-6	0.808	INTERGENIC
3L	10836895	3L_10836895_SNP [dm3] 3L_10843795_SNP [dm6]	A	G	7.025e^-6	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2R	17929699	2R_17929699_SNP [dm3] 2R_22042194_SNP [dm6]	A	G	7.581e^-6	0.808	SYNONYMOUS_CODING PpD5	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	5204026	X_5204026_SNP [dm3] X_5309993_SNP [dm6]	A	T	8.159e^-6	0.808	DOWNSTREAM TrxT INTRON snf	TF binding site BDTNP1_TFBS_dl
2R	9764517	2R_9764517_SNP [dm3] 2R_13877012_SNP [dm6]	C	T	8.553e^-6	0.808	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	17933312	X_17933312_SNP [dm3] X_18039279_SNP [dm6]	G	A	8.687e^-6	0.808	START_GAINED Sh UTR_5_PRIME Sh
X	10751624	X_10751624_SNP [dm3] X_10857591_SNP [dm6]	G	A	8.937e^-6	0.808	UPSTREAM CG2186 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Ubx
2R	9679289	2R_9679289_SNP [dm3] 2R_13791784_SNP [dm6]	T	G	9.078e^-6	0.808	UPSTREAM CR43811 INTERGENIC
2R	17647629	2R_17647629_SNP [dm3] 2R_21760124_SNP [dm6]	T	A	1.096e^-5	0.808	INTERGENIC
3L	16036130	3L_16036130_SNP [dm3] 3L_16043030_SNP [dm6]	C	T	1.110e^-5	0.808	UTR_5_PRIME th UPSTREAM th INTRON th	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_inv
X	10751602	X_10751602_SNP [dm3] X_10857569_SNP [dm6]	G	A	1.226e^-5	0.808	UPSTREAM CG2186 & 1 other INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Ubx
3L	7266474	3L_7266474_SNP [dm3] 3L_7273374_SNP [dm6]	G	A	1.377e^-5	0.808	SYNONYMOUS_CODING unc-13-4A	TF binding site mE1_TFBS_cad
3R	22449876	3R_22449876_SNP [dm3] 3R_26624154_SNP [dm6]	G	T	1.639e^-5	0.808	UPSTREAM TwdlB DOWNSTREAM TwdlL INTERGENIC
2R	15540432	2R_15540432_SNP [dm3] 2R_19652927_SNP [dm6]	C	T	1.643e^-5	0.808	UPSTREAM CR44213 DOWNSTREAM Ir56e EXON CR44212
2R	9799329	2R_9799329_INS [dm3] 2R_13911824_INS [dm6]	A	TGATGGTG	1.792e^-5	0.808	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799332	2R_9799332_SNP [dm3] 2R_13911827_SNP [dm6]	A	G	1.792e^-5	0.808	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799335	2R_9799335_SNP [dm3] 2R_13911830_SNP [dm6]	C	T	1.792e^-5	0.808	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	12074021	2R_12074021_SNP [dm3] 2R_16186516_SNP [dm6]	C	A	1.807e^-5	0.808	UPSTREAM clu & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Ubx
2R	20191493	2R_20191493_SNP [dm3] 2R_24303970_SNP [dm6]	G	A	1.821e^-5	0.808	INTERGENIC	regulatory region REDfly_CRMs
2L	10572922	2L_10572922_SNP [dm3] 2L_10572922_SNP [dm6]	T	C	1.833e^-5	0.808	INTRON Trim9
3R	16300782	3R_16300782_SNP [dm3] 3R_20475060_SNP [dm6]	T	C	1.848e^-5	0.808	INTRON Gfrl
2R	9799311	2R_9799311_SNP [dm3] 2R_13911806_SNP [dm6]	C	T	1.864e^-5	0.808	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	12100255	2R_12100255_SNP [dm3] 2R_16212750_SNP [dm6]	T	C	1.969e^-5	0.808	INTRON mrj
2L	7281732	2L_7281732_SNP [dm3] 2L_7281732_SNP [dm6]	C	T	2.070e^-5	0.808	INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_da mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2L	18814298	2L_18814298_SNP [dm3] 2L_18814298_SNP [dm6]	T	C	2.113e^-5	0.808	DOWNSTREAM CG17325 & 1 other INTERGENIC
2R	9677964	2R_9677964_SNP [dm3] 2R_13790459_SNP [dm6]	A	T	2.118e^-5	0.808	INTERGENIC
X	16925264	X_16925264_SNP [dm3] X_17031231_SNP [dm6]	G	A	2.118e^-5	0.808	INTRON CG45002
2L	8423456	2L_8423456_DEL [dm3] 2L_8423456_DEL [dm6]	TGCT	T	2.207e^-5	0.808	INTRON Akap200	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
2R	5401020	2R_5401020_SNP [dm3] 2R_9513515_SNP [dm6]	A	G	2.263e^-5	0.808	INTRON brp
2L	18814299	2L_18814299_SNP [dm3] 2L_18814299_SNP [dm6]	A	G	2.338e^-5	0.808	DOWNSTREAM CG17325 & 1 other INTERGENIC
3L	9666801	3L_9666801_SNP [dm3] 3L_9673701_SNP [dm6]	A	G	2.359e^-5	0.808	INTRON fry
2R	12073056	2R_12073056_SNP [dm3] 2R_16185551_SNP [dm6]	A	G	2.432e^-5	0.808	SYNONYMOUS_CODING CG8441 DOWNSTREAM Lis-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	19207896	3R_19207896_SNP [dm3] 3R_23382174_SNP [dm6]	T	A	2.493e^-5	0.808	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9286685	2L_9286685_SNP [dm3] 2L_9286685_SNP [dm6]	T	C	2.507e^-5	0.808	INTRON Ggamma30A
3R	10313733	3R_10313733_SNP [dm3] 3R_14488011_SNP [dm6]	G	T	2.515e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	9676653	2R_9676653_SNP [dm3] 2R_13789148_SNP [dm6]	G	A	2.574e^-5	0.808	INTERGENIC
X	5076530	X_5076530_SNP [dm3] X_5182497_SNP [dm6]	C	T	2.606e^-5	0.808	UPSTREAM CG5062 INTRON rg & 1 other
2R	9675391	2R_9675391_SNP [dm3] 2R_13787886_SNP [dm6]	G	A	2.679e^-5	0.808	DOWNSTREAM Cpr50Ca INTERGENIC
3R	20517634	3R_20517634_SNP [dm3] 3R_24691912_SNP [dm6]	C	T	2.703e^-5	0.808	SYNONYMOUS_CODING slo
2R	17647635	2R_17647635_INS [dm3] 2R_21760130_INS [dm6]	C	CC	2.719e^-5	0.808	INTERGENIC
2R	9677957	2R_9677957_SNP [dm3] 2R_13790452_SNP [dm6]	A	T	2.782e^-5	0.808	INTERGENIC
2R	8114799	2R_8114799_SNP [dm3] 2R_12227294_SNP [dm6]	G	A	2.814e^-5	0.808	UPSTREAM CG8854 INTRON CG8854
3R	13283483	3R_13283483_SNP [dm3] 3R_17457761_SNP [dm6]	C	T	2.814e^-5	0.808	UPSTREAM CG14330 INTERGENIC
X	20826251	X_20826251_SNP [dm3] X_20955224_SNP [dm6]	C	T	2.820e^-5	0.808	INTERGENIC
2L	15140673	2L_15140673_SNP [dm3] 2L_15140673_SNP [dm6]	C	T	2.827e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	4132014	2L_4132014_SNP [dm3] 2L_4132014_SNP [dm6]	C	T	2.855e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	17293564	3R_17293564_SNP [dm3] 3R_21467842_SNP [dm6]	C	A	2.973e^-5	0.808	INTERGENIC
3R	17293574	3R_17293574_SNP [dm3] 3R_21467852_SNP [dm6]	A	G	2.973e^-5	0.808	INTERGENIC
3R	17293596	3R_17293596_SNP [dm3] 3R_21467874_SNP [dm6]	T	A	2.973e^-5	0.808	INTERGENIC
X	20824995	X_20824995_INS [dm3] X_20953968_INS [dm6]	A	AAAAAA	2.979e^-5	0.808	INTERGENIC
X	20824984	X_20824984_SNP [dm3] X_20953957_SNP [dm6]	T	C	3.042e^-5	0.808	INTERGENIC
3R	17293551	3R_17293551_SNP [dm3] 3R_21467829_SNP [dm6]	T	G	3.045e^-5	0.808	INTERGENIC
2R	20191583	2R_20191583_SNP [dm3] 2R_24304060_SNP [dm6]	C	G	3.106e^-5	0.808	INTERGENIC	regulatory region REDfly_CRMs
2R	3346733	2R_3346733_DEL [dm3] 2R_7459228_DEL [dm6]	TA	T	3.126e^-5	0.808	UPSTREAM Inos DOWNSTREAM CG11141 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	1534413	2R_1534413_SNP [dm3] 2R_5646908_SNP [dm6]	T	C	3.153e^-5	0.808	INTRON CG11665
3L	12564316	3L_12564316_SNP [dm3] 3L_12571216_SNP [dm6]	G	A	3.205e^-5	0.808	INTRON sowah	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	9679404	2R_9679404_SNP [dm3] 2R_13791899_SNP [dm6]	G	A	3.333e^-5	0.808	UPSTREAM CR43811 INTERGENIC
2R	10033162	2R_10033162_SNP [dm3] 2R_14145657_SNP [dm6]	T	A	3.362e^-5	0.808	UPSTREAM mir-989 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3R	17293603	3R_17293603_SNP [dm3] 3R_21467881_SNP [dm6]	C	T	3.383e^-5	0.808	INTERGENIC
2R	12073825	2R_12073825_DEL [dm3] 2R_16186320_DEL [dm6]	CCTCAACGACGC...	A	3.445e^-5	0.808	UPSTREAM clu & 1 other INTRON CG8441	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	9677994	2R_9677994_SNP [dm3] 2R_13790489_SNP [dm6]	T	A	3.513e^-5	0.808	INTERGENIC	TF binding site mE1_TFBS_cad
2R	19573384	2R_19573384_SNP [dm3] 2R_23685861_SNP [dm6]	T	A	3.533e^-5	0.808	UPSTREAM l_2_efl INTRON St3
3R	8147882	3R_8147882_SNP [dm3] 3R_12322160_SNP [dm6]	C	T	3.690e^-5	0.808	DOWNSTREAM tRNA:CR31432 INTERGENIC
2R	9677979	2R_9677979_SNP [dm3] 2R_13790474_SNP [dm6]	T	A	3.717e^-5	0.808	INTERGENIC
3L	7769451	3L_7769451_SNP [dm3] 3L_7776351_SNP [dm6]	A	T	3.773e^-5	0.808	UPSTREAM Clk DOWNSTREAM CG32369 INTERGENIC	regulatory region REDfly_CRMs
2R	9675072	2R_9675072_SNP [dm3] 2R_13787567_SNP [dm6]	A	C	3.793e^-5	0.808	UTR_3_PRIME Cpr50Ca
X	16925193	X_16925193_SNP [dm3] X_17031160_SNP [dm6]	A	T	3.800e^-5	0.808	INTRON CG45002
3R	26088906	3R_26088906_SNP [dm3] 3R_30263184_SNP [dm6]	C	T	3.810e^-5	0.808	INTERGENIC
3R	10313668	3R_10313668_SNP [dm3] 3R_14487946_SNP [dm6]	T	C	3.847e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	12073840	2R_12073840_SNP [dm3] 2R_16186335_SNP [dm6]	T	A	3.994e^-5	0.808	UPSTREAM clu & 1 other INTRON CG8441	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	10836651	3L_10836651_SNP [dm3] 3L_10843551_SNP [dm6]	C	T	4.014e^-5	0.808	INTERGENIC	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	3979536	X_3979536_SNP [dm3] X_4085503_SNP [dm6]	A	C	4.048e^-5	0.808	INTRON CG43689
X	10751574	X_10751574_SNP [dm3] X_10857541_SNP [dm6]	T	C	4.081e^-5	0.808	UPSTREAM CG2186 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Ubx
X	1221985	X_1221985_SNP [dm3] X_1327952_SNP [dm6]	G	A	4.148e^-5	0.808	SYNONYMOUS_CODING fs_1_N
2R	2452853	2R_2452853_SNP [dm3] 2R_6565348_SNP [dm6]	A	G	4.225e^-5	0.808	INTRON jing
3R	25483333	3R_25483333_SNP [dm3] 3R_29657611_SNP [dm6]	G	C	4.228e^-5	0.808	INTRON Dop1R2
X	15204317	X_15204317_SNP [dm3] X_15310284_SNP [dm6]	T	C	4.231e^-5	0.808	INTRON gce
2L	13058490	2L_13058490_SNP [dm3] 2L_13058490_SNP [dm6]	C	G	4.308e^-5	0.808	INTRON CG9932
3R	25485391	3R_25485391_SNP [dm3] 3R_29659669_SNP [dm6]	G	A	4.320e^-5	0.808	INTRON Dop1R2
3L	12564309	3L_12564309_SNP [dm3] 3L_12571209_SNP [dm6]	C	A	4.340e^-5	0.808	INTRON sowah	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	17292496	2L_17292496_DEL [dm3] 2L_17292496_DEL [dm6]	AA	A	4.381e^-5	0.808	UPSTREAM CG6380 INTERGENIC
2R	10033109	2R_10033109_SNP [dm3] 2R_14145604_SNP [dm6]	C	T	4.394e^-5	0.808	UPSTREAM mir-989 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	7154304	3L_7154304_SNP [dm3] 3L_7161204_SNP [dm6]	T	A	4.437e^-5	0.808	UTR_3_PRIME Dscam2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	18964592	X_18964592_SNP [dm3] X_19070559_SNP [dm6]	T	C	4.481e^-5	0.808	INTERGENIC
2L	9079049	2L_9079049_SNP [dm3] 2L_9079049_SNP [dm6]	G	C	4.492e^-5	0.808	INTERGENIC
2L	18820270	2L_18820270_SNP [dm3] 2L_18820270_SNP [dm6]	T	C	4.559e^-5	0.808	SYNONYMOUS_CODING CG17324	TF binding site mE1_TFBS_cad
3L	7154297	3L_7154297_SNP [dm3] 3L_7161197_SNP [dm6]	T	G	4.600e^-5	0.808	UTR_3_PRIME Dscam2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	10430998	2L_10430998_SNP [dm3] 2L_10430998_SNP [dm6]	T	A	4.615e^-5	0.808	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	14791656	2R_14791656_SNP [dm3] 2R_18904151_SNP [dm6]	G	T	4.732e^-5	0.808	INTRON sano	TF binding site BDTNP1_TFBS_dl
2R	9675820	2R_9675820_SNP [dm3] 2R_13788315_SNP [dm6]	T	A	4.749e^-5	0.808	DOWNSTREAM Cpr50Ca INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

mn_Life_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results