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=8.430e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1872 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
3R	18163375	3R_18163375_SNP [dm3] 3R_22337653_SNP [dm6]	T	C	1.533e^-7	0.287	INTRON CG5388
3L	10893471	3L_10893471_SNP [dm3] 3L_10900371_SNP [dm6]	G	A	6.069e^-7	0.291	INTERGENIC
3L	10892043	3L_10892043_SNP [dm3] 3L_10898943_SNP [dm6]	G	A	7.754e^-7	0.291	UTR_5_PRIME Aps UPSTREAM Aps	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	10892323	3L_10892323_SNP [dm3] 3L_10899223_SNP [dm6]	C	T	7.754e^-7	0.291	UPSTREAM Aps INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	10892370	3L_10892370_SNP [dm3] 3L_10899270_SNP [dm6]	A	T	7.754e^-7	0.291	UPSTREAM Aps INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	10890072	3L_10890072_SNP [dm3] 3L_10896972_SNP [dm6]	C	A	1.013e^-6	0.317	INTRON Aps
2L	17250475	2L_17250475_SNP [dm3] 2L_17250475_SNP [dm6]	T	C	1.449e^-6	0.388	INTRON beat-IIIc	TF binding site mE1_TFBS_HSA mE1_TFBS_run
3L	10893186	3L_10893186_SNP [dm3] 3L_10900086_SNP [dm6]	C	G	1.993e^-6	0.463	UPSTREAM Aps INTERGENIC	TF binding site mE1_TFBS_sens
3L	10892347	3L_10892347_SNP [dm3] 3L_10899247_SNP [dm6]	T	A	2.226e^-6	0.463	UPSTREAM Aps INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	7232323	3L_7232323_SNP [dm3] 3L_7239223_SNP [dm6]	G	T	2.604e^-6	0.488	NON_SYNONYMOUS_CODING BHD DOWNSTREAM RpL18	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	3373038	3R_3373038_SNP [dm3] 3R_7547316_SNP [dm6]	A	C	3.641e^-6	0.586	INTRON alpha-Est1	TF binding site mE1_TFBS_cad
3L	7233131	3L_7233131_SNP [dm3] 3L_7240031_SNP [dm6]	A	C	3.751e^-6	0.586	DOWNSTREAM RpL18 INTRON BHD	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	10888831	3L_10888831_SNP [dm3] 3L_10895731_SNP [dm6]	C	T	4.918e^-6	0.709	UTR_3_PRIME Aps UPSTREAM CR45171
2L	14698866	2L_14698866_SNP [dm3] 2L_14698866_SNP [dm6]	T	C	6.886e^-6	0.895	INTERGENIC
2L	4313922	2L_4313922_SNP [dm3] 2L_4313922_SNP [dm6]	A	T	8.887e^-6	0.895	INTRON tutl
3R	19053367	3R_19053367_SNP [dm3] 3R_23227645_SNP [dm6]	G	T	8.966e^-6	0.895	UPSTREAM cnc DOWNSTREAM CG4467 INTERGENIC
2L	15779410	2L_15779410_SNP [dm3] 2L_15779410_SNP [dm6]	G	T	9.915e^-6	0.895	INTERGENIC
2L	4402131	2L_4402131_SNP [dm3] 2L_4402131_SNP [dm6]	A	T	1.022e^-5	0.895	SYNONYMOUS_CODING CG33003	TF binding site mE1_TFBS_cad
3L	10893148	3L_10893148_SNP [dm3] 3L_10900048_SNP [dm6]	G	A	1.036e^-5	0.895	UPSTREAM Aps INTERGENIC	TF binding site mE1_TFBS_sens
3R	9970520	3R_9970520_SNP [dm3] 3R_14144798_SNP [dm6]	A	T	1.041e^-5	0.895	INTERGENIC
2L	14459111	2L_14459111_SNP [dm3] 2L_14459111_SNP [dm6]	T	G	1.047e^-5	0.895	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
X	1043306	X_1043306_SNP [dm3] X_1149273_SNP [dm6]	G	A	1.087e^-5	0.895	INTERGENIC
2L	7153015	2L_7153015_SNP [dm3] 2L_7153015_SNP [dm6]	A	C	1.178e^-5	0.895	INTRON Pvf3
2R	10853979	2R_10853979_SNP [dm3] 2R_14966474_SNP [dm6]	A	G	1.192e^-5	0.895	INTRON ckn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14416664	2L_14416664_SNP [dm3] 2L_14416664_SNP [dm6]	G	A	1.286e^-5	0.895	DOWNSTREAM Pburs INTERGENIC
3R	11124169	3R_11124169_SNP [dm3] 3R_15298447_SNP [dm6]	G	A	1.292e^-5	0.895	DOWNSTREAM Tm1 INTRON Tm1
3L	9566166	3L_9566166_SNP [dm3] 3L_9573066_SNP [dm6]	T	A	1.314e^-5	0.895	INTRON CG42673
3L	10890463	3L_10890463_SNP [dm3] 3L_10897363_SNP [dm6]	C	G	1.337e^-5	0.895	INTRON Aps
3R	18163547	3R_18163547_SNP [dm3] 3R_22337825_SNP [dm6]	A	G	1.445e^-5	0.899	INTRON CG5388
3L	10890417	3L_10890417_SNP [dm3] 3L_10897317_SNP [dm6]	C	G	1.447e^-5	0.899	INTRON Aps
3L	10890410	3L_10890410_SNP [dm3] 3L_10897310_SNP [dm6]	A	G	1.600e^-5	0.899	INTRON Aps
3L	891427	3L_891427_SNP [dm3] 3L_891427_SNP [dm6]	A	G	1.626e^-5	0.899	DOWNSTREAM snoRNA:CG32479-b INTRON CG32479 EXON snoRNA:CG32479-a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	12985683	3L_12985683_SNP [dm3] 3L_12992583_SNP [dm6]	A	G	1.632e^-5	0.899	INTERGENIC
2L	14459119	2L_14459119_SNP [dm3] 2L_14459119_SNP [dm6]	T	A	1.658e^-5	0.899	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
3L	10891447	3L_10891447_SNP [dm3] 3L_10898347_SNP [dm6]	C	T	1.701e^-5	0.899	UTR_5_PRIME Aps	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl mE1_TFBS_zfh1
3L	7233047	3L_7233047_SNP [dm3] 3L_7239947_SNP [dm6]	G	A	1.727e^-5	0.899	SYNONYMOUS_CODING BHD DOWNSTREAM RpL18	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	1007898	X_1007898_SNP [dm3] X_1113865_SNP [dm6]	A	G	1.875e^-5	0.909	INTRON CG3655
3L	10885514	3L_10885514_SNP [dm3] 3L_10892414_SNP [dm6]	A	G	1.977e^-5	0.909	UTR_3_PRIME Cpr67Fa2
3L	7130471	3L_7130471_SNP [dm3] 3L_7137371_SNP [dm6]	G	A	2.046e^-5	0.909	INTRON melt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA
3R	24582240	3R_24582240_SNP [dm3] 3R_28756518_SNP [dm6]	T	A	2.183e^-5	0.909	NON_SYNONYMOUS_CODING CG9997 DOWNSTREAM aqrs	TF binding site BDTNP1_TFBS_bcd
2R	10717953	2R_10717953_SNP [dm3] 2R_14830448_SNP [dm6]	T	C	2.203e^-5	0.909	INTERGENIC
3R	22064050	3R_22064050_SNP [dm3] 3R_26238328_SNP [dm6]	A	G	2.214e^-5	0.909	INTRON CR42745
3L	12357958	3L_12357958_SNP [dm3] 3L_12364858_SNP [dm6]	T	G	2.236e^-5	0.909	INTERGENIC
2L	4313899	2L_4313899_SNP [dm3] 2L_4313899_SNP [dm6]	T	A	2.325e^-5	0.909	INTRON tutl
2R	16231363	2R_16231363_SNP [dm3] 2R_20343858_SNP [dm6]	A	T	2.399e^-5	0.909	UTR_5_PRIME CG13870	TF binding site mE1_TFBS_inv
2R	10853857	2R_10853857_SNP [dm3] 2R_14966352_SNP [dm6]	T	A	2.455e^-5	0.909	INTRON ckn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	17251487	2L_17251487_SNP [dm3] 2L_17251487_SNP [dm6]	A	C	2.492e^-5	0.909	INTRON beat-IIIc
2L	17251915	2L_17251915_SNP [dm3] 2L_17251915_SNP [dm6]	C	G	2.492e^-5	0.909	INTRON beat-IIIc
2L	17250811	2L_17250811_SNP [dm3] 2L_17250811_SNP [dm6]	C	A	2.531e^-5	0.909	INTRON beat-IIIc	TF binding site mE1_TFBS_run
2L	14575697	2L_14575697_SNP [dm3] 2L_14575697_SNP [dm6]	G	A	2.560e^-5	0.909	UPSTREAM CR44856 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	10872518	3L_10872518_SNP [dm3] 3L_10879418_SNP [dm6]	A	T	2.655e^-5	0.909	SYNONYMOUS_CODING Blos4 UPSTREAM CG6418	TF binding site BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	14416640	2L_14416640_SNP [dm3] 2L_14416640_SNP [dm6]	A	G	2.714e^-5	0.909	DOWNSTREAM Pburs INTERGENIC
3L	11043204	3L_11043204_SNP [dm3] 3L_11050104_SNP [dm6]	G	A	2.763e^-5	0.909	UPSTREAM CR45119 INTRON CG43693
2R	10853884	2R_10853884_SNP [dm3] 2R_14966379_SNP [dm6]	A	G	2.881e^-5	0.909	INTRON ckn	TF binding site mE1_TFBS_HSA
2L	14416677	2L_14416677_SNP [dm3] 2L_14416677_SNP [dm6]	C	T	2.984e^-5	0.909	DOWNSTREAM Pburs INTERGENIC
2R	18467306	2R_18467306_SNP [dm3] 2R_22579801_SNP [dm6]	A	T	3.042e^-5	0.909	INTRON dnr1
3R	18163548	3R_18163548_SNP [dm3] 3R_22337826_SNP [dm6]	A	C	3.063e^-5	0.909	INTRON CG5388
3L	658425	3L_658425_SNP [dm3] 3L_658425_SNP [dm6]	A	G	3.064e^-5	0.909	DOWNSTREAM Rev1 INTERGENIC
2L	17787810	2L_17787810_SNP [dm3] 2L_17787810_SNP [dm6]	T	G	3.100e^-5	0.909	UTR_3_PRIME CadN2
2L	4489447	2L_4489447_SNP [dm3] 2L_4489447_SNP [dm6]	C	A	3.138e^-5	0.909	INTRON dp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3R	22064055	3R_22064055_SNP [dm3] 3R_26238333_SNP [dm6]	G	A	3.154e^-5	0.909	INTRON CR42745
3L	10895067	3L_10895067_SNP [dm3] 3L_10901967_SNP [dm6]	A	T	3.240e^-5	0.909	INTERGENIC
3L	10874204	3L_10874204_SNP [dm3] 3L_10881104_SNP [dm6]	C	T	3.292e^-5	0.909	SYNONYMOUS_CODING CG6409 DOWNSTREAM Blos4	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	14423078	2L_14423078_SNP [dm3] 2L_14423078_SNP [dm6]	A	T	3.322e^-5	0.909	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	17251110	2L_17251110_SNP [dm3] 2L_17251110_SNP [dm6]	A	G	3.330e^-5	0.909	INTRON beat-IIIc
3L	8643588	3L_8643588_SNP [dm3] 3L_8650488_SNP [dm6]	A	C	3.346e^-5	0.909	INTRON Pex7	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19892747	2R_19892747_INS [dm3] 2R_24005224_INS [dm6]	A	AAGG	3.515e^-5	0.909	INTRON Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	16973325	2L_16973325_SNP [dm3] 2L_16973325_SNP [dm6]	A	T	3.523e^-5	0.909	START_GAINED beat-IIIb UTR_5_PRIME beat-IIIb	TF binding site mE1_TFBS_Trl
2R	8785492	2R_8785492_SNP [dm3] 2R_12897987_SNP [dm6]	G	A	3.560e^-5	0.909	INTRON vg	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	875928	3L_875928_SNP [dm3] 3L_875928_SNP [dm6]	G	T	3.567e^-5	0.909	INTRON CG32479	TF binding site mE1_TFBS_HSA
3R	25299195	3R_25299195_SNP [dm3] 3R_29473473_SNP [dm6]	C	T	3.604e^-5	0.909	INTRON Ptp99A
3L	9628731	3L_9628731_SNP [dm3] 3L_9635631_SNP [dm6]	C	G	3.750e^-5	0.909	INTRON fry
3R	13666443	3R_13666443_SNP [dm3] 3R_17840721_SNP [dm6]	T	C	3.760e^-5	0.909	INTRON tinc
3L	891421	3L_891421_SNP [dm3] 3L_891421_SNP [dm6]	T	A	3.782e^-5	0.909	DOWNSTREAM snoRNA:CG32479-b INTRON CG32479 EXON snoRNA:CG32479-a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	24275459	3R_24275459_SNP [dm3] 3R_28449737_SNP [dm6]	T	A	3.796e^-5	0.909	INTRON beat-VI
X	8510598	X_8510598_SNP [dm3] X_8616565_SNP [dm6]	T	A	3.835e^-5	0.909	INTERGENIC
3L	10970965	3L_10970965_SNP [dm3] 3L_10977865_SNP [dm6]	A	G	3.853e^-5	0.909	DOWNSTREAM CR45745 INTERGENIC
2R	4156946	2R_4156946_SNP [dm3] 2R_8269441_SNP [dm6]	G	C	3.919e^-5	0.909	UPSTREAM CG30371 INTERGENIC
2R	10853895	2R_10853895_SNP [dm3] 2R_14966390_SNP [dm6]	T	C	3.922e^-5	0.909	INTRON ckn	TF binding site mE1_TFBS_HSA
X	1043304	X_1043304_SNP [dm3] X_1149271_SNP [dm6]	T	A	4.061e^-5	0.909	INTERGENIC
3L	10890437	3L_10890437_SNP [dm3] 3L_10897337_SNP [dm6]	A	C	4.071e^-5	0.909	INTRON Aps
3L	10890455	3L_10890455_SNP [dm3] 3L_10897355_SNP [dm6]	A	C	4.071e^-5	0.909	INTRON Aps
2R	16231367	2R_16231367_SNP [dm3] 2R_20343862_SNP [dm6]	T	C	4.094e^-5	0.909	UTR_5_PRIME CG13870	TF binding site mE1_TFBS_inv
3L	18541711	3L_18541711_SNP [dm3] 3L_18548611_SNP [dm6]	G	A	4.132e^-5	0.909	INTERGENIC
3L	18498146	3L_18498146_SNP [dm3] 3L_18505046_SNP [dm6]	C	T	4.162e^-5	0.909	INTERGENIC
3L	18543458	3L_18543458_INS [dm3] 3L_18550358_INS [dm6]	C	CTGGGC	4.178e^-5	0.909	INTERGENIC
X	9485492	X_9485492_SNP [dm3] X_9591459_SNP [dm6]	C	G	4.352e^-5	0.909	UPSTREAM CR45542 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	1043298	X_1043298_INS [dm3] X_1149265_INS [dm6]	A	AACACGTCGATCCTCGTCCT...	4.392e^-5	0.909	INTERGENIC
3L	13934700	3L_13934700_SNP [dm3] 3L_13941600_SNP [dm6]	G	A	4.603e^-5	0.909	INTRON CG32137	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3R	12251436	3R_12251436_DEL [dm3] 3R_16425714_DEL [dm6]	TT	T	4.661e^-5	0.909	UPSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
X	1043294	X_1043294_SNP [dm3] X_1149261_SNP [dm6]	A	G	4.709e^-5	0.909	INTERGENIC
3L	7229359	3L_7229359_SNP [dm3] 3L_7236259_SNP [dm6]	T	C	4.726e^-5	0.909	DOWNSTREAM CG14826 & 1 other INTERGENIC
X	1007565	X_1007565_SNP [dm3] X_1113532_SNP [dm6]	G	T	4.764e^-5	0.909	INTRON CG3655
3R	5260745	3R_5260745_SNP [dm3] 3R_9435023_SNP [dm6]	T	G	4.768e^-5	0.909	INTRON ps	TF binding site mE1_TFBS_cad
3R	3464383	3R_3464383_SNP [dm3] 3R_7638661_SNP [dm6]	G	T	4.801e^-5	0.909	INTRON CG34127
2R	16231369	2R_16231369_SNP [dm3] 2R_20343864_SNP [dm6]	G	T	4.846e^-5	0.909	START_GAINED CG13870 UTR_5_PRIME CG13870	TF binding site mE1_TFBS_inv
3R	4959269	3R_4959269_SNP [dm3] 3R_9133547_SNP [dm6]	C	A	4.908e^-5	0.909	INTRON pum
2R	16231296	2R_16231296_SNP [dm3] 2R_20343791_SNP [dm6]	T	G	4.937e^-5	0.909	UPSTREAM CG13870 INTERGENIC
2L	21154147	2L_21154147_INS [dm3] 2L_21154147_INS [dm6]	A	ACAA	4.957e^-5	0.909	DOWNSTREAM E2f2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2R	10853864	2R_10853864_SNP [dm3] 2R_14966359_SNP [dm6]	T	C	4.987e^-5	0.909	INTRON ckn	TF binding site mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

PC5_Nutri_Score_Low phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results