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=5.945e^-2)
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

1591 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	18092484	2R_18092484_SNP [dm3] 2R_22204979_SNP [dm6]	G	A	3.802e^-7	0.383	SYNONYMOUS_CODING CG3292
2R	19535680	2R_19535680_SNP [dm3] 2R_23648157_SNP [dm6]	G	A	5.813e^-7	0.383	INTRON retn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	18092521	2R_18092521_SNP [dm3] 2R_22205016_SNP [dm6]	G	T	7.865e^-7	0.383	DOWNSTREAM CG3290 INTRON CG3292
3L	18580422	3L_18580422_SNP [dm3] 3L_18587322_SNP [dm6]	G	A	1.014e^-6	0.383	INTERGENIC
2R	18092508	2R_18092508_SNP [dm3] 2R_22205003_SNP [dm6]	T	G	1.022e^-6	0.383	SPLICE_SITE_REGION CG3292 SYNONYMOUS_CODING CG3292
2L	2527756	2L_2527756_SNP [dm3] 2L_2527756_SNP [dm6]	T	G	1.445e^-6	0.451	INTERGENIC
3L	10309822	3L_10309822_SNP [dm3] 3L_10316722_SNP [dm6]	A	C	2.122e^-6	0.568	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	18092514	2R_18092514_SNP [dm3] 2R_22205009_SNP [dm6]	C	A	3.045e^-6	0.642	SPLICE_SITE_REGION CG3292 DOWNSTREAM CG3290 INTRON CG3292
3L	1046141	3L_1046141_SNP [dm3] 3L_1046141_SNP [dm6]	C	T	3.084e^-6	0.642	INTRON bab1
2L	3355667	2L_3355667_DEL [dm3] 2L_3355667_DEL [dm6]	TTCT	T	3.463e^-6	0.649	UPSTREAM E23 INTERGENIC	TF binding site mE1_TFBS_Trl
X	2516882	X_2516882_SNP [dm3] X_2622849_SNP [dm6]	G	A	4.197e^-6	0.65	SYNONYMOUS_CODING brv3 DOWNSTREAM Seipin	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	2536566	X_2536566_SNP [dm3] X_2642533_SNP [dm6]	A	G	4.297e^-6	0.65	UPSTREAM sgg INTRON sgg	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	3259797	3L_3259797_SNP [dm3] 3L_3259797_SNP [dm6]	T	G	4.508e^-6	0.65	INTRON ckd
2R	18091233	2R_18091233_SNP [dm3] 2R_22203728_SNP [dm6]	A	T	4.974e^-6	0.666	UTR_3_PRIME CG3292 DOWNSTREAM CR45376
2L	3786563	2L_3786563_SNP [dm3] 2L_3786563_SNP [dm6]	G	C	5.520e^-6	0.69	UPSTREAM CG3921 DOWNSTREAM CG31960 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
2L	9663453	2L_9663453_DEL [dm3] 2L_9663453_DEL [dm6]	CC	C	6.106e^-6	0.7	INTERGENIC
2R	18099434	2R_18099434_SNP [dm3] 2R_22211929_SNP [dm6]	C	T	6.345e^-6	0.7	SYNONYMOUS_CODING CG11291 UPSTREAM ari-2	TF binding site mE1_TFBS_sens
3L	18580449	3L_18580449_SNP [dm3] 3L_18587349_SNP [dm6]	A	T	6.882e^-6	0.717	INTERGENIC
3L	3694006	3L_3694006_SNP [dm3] 3L_3694006_SNP [dm6]	T	G	8.114e^-6	0.791	EXON CR43485
2L	12419457	2L_12419457_SNP [dm3] 2L_12419457_SNP [dm6]	T	G	8.441e^-6	0.791	INTRON vir-1
2R	16310981	2R_16310981_SNP [dm3] 2R_20423476_SNP [dm6]	T	C	1.044e^-5	0.932	UPSTREAM CG12484 INTERGENIC
2R	1356376	2R_1356376_SNP [dm3] 2R_5468871_SNP [dm6]	T	C	1.220e^-5	1	INTRON CG30440
3L	3706261	3L_3706261_SNP [dm3] 3L_3706261_SNP [dm6]	A	C	1.287e^-5	1	INTERGENIC
3L	18580404	3L_18580404_DEL [dm3] 3L_18587304_DEL [dm6]	TTTCCTGGT	T	1.379e^-5	1	INTERGENIC
2R	18042418	2R_18042418_SNP [dm3] 2R_22154913_SNP [dm6]	T	A	1.437e^-5	1	INTRON a	TF binding site BDTNP1_TFBS_da
3L	1469433	3L_1469433_SNP [dm3] 3L_1469433_SNP [dm6]	T	A	1.612e^-5	1	DOWNSTREAM rho INTRON Ptp61F
2R	18090768	2R_18090768_SNP [dm3] 2R_22203263_SNP [dm6]	C	A	1.637e^-5	1	UPSTREAM Swim DOWNSTREAM CG3292 & 1 other INTERGENIC
2R	18095929	2R_18095929_SNP [dm3] 2R_22208424_SNP [dm6]	C	T	1.727e^-5	1	UPSTREAM CG3290 DOWNSTREAM CG3264 INTERGENIC	TF binding site mE1_TFBS_HSA
2L	9663560	2L_9663560_SNP [dm3] 2L_9663560_SNP [dm6]	G	T	1.810e^-5	1	INTERGENIC
3R	19178496	3R_19178496_SNP [dm3] 3R_23352774_SNP [dm6]	A	G	2.039e^-5	1	SYNONYMOUS_CODING DNApol-epsilon	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23165564	3R_23165564_SNP [dm3] 3R_27339842_SNP [dm6]	G	A	2.219e^-5	1	UPSTREAM CG42534 INTERGENIC
3L	297694	3L_297694_SNP [dm3] 3L_297694_SNP [dm6]	C	T	2.253e^-5	1	UPSTREAM RhoGEF3 INTRON RhoGEF3	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_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	298038	3L_298038_SNP [dm3] 3L_298038_SNP [dm6]	A	C	2.253e^-5	1	NON_SYNONYMOUS_CODING RhoGEF3 INTRON RhoGEF3	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 BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	18378411	3R_18378411_SNP [dm3] 3R_22552689_SNP [dm6]	A	G	2.271e^-5	1	UPSTREAM bond & 1 other INTRON bond
X	19241123	X_19241123_SNP [dm3] X_19347090_SNP [dm6]	C	T	2.301e^-5	1	INTRON nAChRalpha7
3L	3706392	3L_3706392_SNP [dm3] 3L_3706392_SNP [dm6]	G	A	2.311e^-5	1	INTERGENIC
2L	3859876	2L_3859876_DEL [dm3] 2L_3859876_DEL [dm6]	TT	T	2.341e^-5	1	INTERGENIC
2R	8901136	2R_8901136_SNP [dm3] 2R_13013631_SNP [dm6]	T	C	2.369e^-5	1	INTERGENIC	TF binding site mE1_TFBS_Trl
3R	26028905	3R_26028905_SNP [dm3] 3R_30203183_SNP [dm6]	C	T	2.598e^-5	1	UPSTREAM CG9743 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	8877016	3L_8877016_SNP [dm3] 3L_8883916_SNP [dm6]	A	G	2.715e^-5	1	INTRON dally
X	10812271	X_10812271_SNP [dm3] X_10918238_SNP [dm6]	C	A	2.723e^-5	1	SYNONYMOUS_CODING CG43901	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18095710	2R_18095710_SNP [dm3] 2R_22208205_SNP [dm6]	A	T	2.747e^-5	1	UPSTREAM CG3290 DOWNSTREAM CG3264 INTERGENIC	TF binding site mE1_TFBS_HSA
3R	23165421	3R_23165421_SNP [dm3] 3R_27339699_SNP [dm6]	C	T	2.866e^-5	1	UPSTREAM CG42534 INTERGENIC
2R	18092535	2R_18092535_SNP [dm3] 2R_22205030_SNP [dm6]	C	G	2.885e^-5	1	DOWNSTREAM CG3290 INTRON CG3292
2R	18092541	2R_18092541_SNP [dm3] 2R_22205036_SNP [dm6]	T	C	2.885e^-5	1	DOWNSTREAM CG3290 INTRON CG3292
2R	18095939	2R_18095939_SNP [dm3] 2R_22208434_SNP [dm6]	G	A	3.073e^-5	1	UPSTREAM CG3290 DOWNSTREAM CG3264 INTERGENIC	TF binding site mE1_TFBS_HSA
3R	26028916	3R_26028916_INS [dm3] 3R_30203194_INS [dm6]	C	CTCCCC	3.200e^-5	1	UPSTREAM CG9743 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	5231259	2L_5231259_SNP [dm3] 2L_5231259_SNP [dm6]	T	C	3.245e^-5	1	INTRON tkv	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	290190	3L_290190_SNP [dm3] 3L_290190_SNP [dm6]	T	C	3.262e^-5	1	SYNONYMOUS_CODING RhoGEF3
3R	25910123	3R_25910123_SNP [dm3] 3R_30084401_SNP [dm6]	T	C	3.293e^-5	1	INTRON sima	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	1277524	3L_1277524_SNP [dm3] 3L_1277524_SNP [dm6]	C	T	3.421e^-5	1	INTRON CG32333
3L	13945259	3L_13945259_SNP [dm3] 3L_13952159_SNP [dm6]	T	A	3.432e^-5	1	INTRON CG32137
3L	305503	3L_305503_SNP [dm3] 3L_305503_SNP [dm6]	A	T	3.483e^-5	1	UTR_3_PRIME fwd DOWNSTREAM fwd & 1 other
3L	3955550	3L_3955550_SNP [dm3] 3L_3955550_SNP [dm6]	C	T	3.504e^-5	1	UTR_3_PRIME CG12605
2R	18098500	2R_18098500_SNP [dm3] 2R_22210995_SNP [dm6]	T	A	3.573e^-5	1	UPSTREAM CG11291 & 1 other INTERGENIC
3L	10309840	3L_10309840_SNP [dm3] 3L_10316740_SNP [dm6]	A	G	3.704e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	4297737	3L_4297737_SNP [dm3] 3L_4297737_SNP [dm6]	C	A	3.789e^-5	1	INTRON dyl
3R	23190890	3R_23190890_SNP [dm3] 3R_27365168_SNP [dm6]	G	C	4.184e^-5	1	INTRON CG42534
2L	9620486	2L_9620486_SNP [dm3] 2L_9620486_SNP [dm6]	G	A	4.216e^-5	1	INTRON GlcAT-S
2L	6045631	2L_6045631_SNP [dm3] 2L_6045631_SNP [dm6]	T	G	4.392e^-5	1	UPSTREAM ade2 DOWNSTREAM mir-966 & 1 other INTRON ade2 EXON mir-966	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9689492	2R_9689492_SNP [dm3] 2R_13801987_SNP [dm6]	T	C	4.609e^-5	1	INTRON Cpr50Cb
2R	19535238	2R_19535238_SNP [dm3] 2R_23647715_SNP [dm6]	G	A	4.649e^-5	1	SYNONYMOUS_CODING retn	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	9424086	3L_9424086_SNP [dm3] 3L_9430986_SNP [dm6]	T	A	4.829e^-5	1	SYNONYMOUS_CODING MTF-1 UTR_5_PRIME MTF-1 INTRON MTF-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	9663400	2L_9663400_SNP [dm3] 2L_9663400_SNP [dm6]	A	T	4.832e^-5	1	INTERGENIC
2L	12161241	2L_12161241_SNP [dm3] 2L_12161241_SNP [dm6]	G	A	4.877e^-5	1	SPLICE_SITE_REGION CG31760 UPSTREAM CG31861 INTRON CG31760
X	9501872	X_9501872_SNP [dm3] X_9607839_SNP [dm6]	A	G	4.996e^-5	1	SYNONYMOUS_CODING Aats-lys	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2L	9665883	2L_9665883_SNP [dm3] 2L_9665883_SNP [dm6]	T	C	5.198e^-5	1	INTERGENIC
2L	8043395	2L_8043395_SNP [dm3] 2L_8043395_SNP [dm6]	G	A	5.238e^-5	1	UPSTREAM CG7466 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
2R	18098498	2R_18098498_SNP [dm3] 2R_22210993_SNP [dm6]	G	T	5.314e^-5	1	UPSTREAM CG11291 & 1 other INTERGENIC
3L	8252533	3L_8252533_SNP [dm3] 3L_8259433_SNP [dm6]	C	A	5.443e^-5	1	INTRON Dscam4
3L	9335730	3L_9335730_SNP [dm3] 3L_9342630_SNP [dm6]	T	C	5.532e^-5	1	SYNONYMOUS_CODING PGRP-LC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	19178520	3R_19178520_SNP [dm3] 3R_23352798_SNP [dm6]	A	G	5.597e^-5	1	SYNONYMOUS_CODING DNApol-epsilon	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	10018367	X_10018367_SNP [dm3] X_10124334_SNP [dm6]	A	T	5.607e^-5	1	UPSTREAM snoRNA:Me18S-A627 INTRON CR44894 & 1 other
2R	18099723	2R_18099723_SNP [dm3] 2R_22212218_SNP [dm6]	C	T	5.757e^-5	1	UPSTREAM ari-2 INTRON CG11291	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	2670266	2L_2670266_SNP [dm3] 2L_2670266_SNP [dm6]	G	A	5.812e^-5	1	SYNONYMOUS_CODING Gr23a UPSTREAM Gr23a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	1277641	3L_1277641_SNP [dm3] 3L_1277641_SNP [dm6]	C	T	5.813e^-5	1	INTRON CG32333
2L	8490609	2L_8490609_SNP [dm3] 2L_8490609_SNP [dm6]	T	G	5.843e^-5	1	UPSTREAM CG43400 DOWNSTREAM CG13088 INTERGENIC
3R	26520251	3R_26520251_SNP [dm3] 3R_30694529_SNP [dm6]	T	C	5.885e^-5	1	SYNONYMOUS_CODING CG12069
X	14709319	X_14709319_SNP [dm3] X_14815286_SNP [dm6]	T	A	5.926e^-5	1	INTRON rut
X	19218874	X_19218874_SNP [dm3] X_19324841_SNP [dm6]	T	C	5.959e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv
2L	3355408	2L_3355408_SNP [dm3] 2L_3355408_SNP [dm6]	C	T	6.051e^-5	1	UPSTREAM E23 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	6094041	3L_6094041_SNP [dm3] 3L_6100941_SNP [dm6]	C	A	6.088e^-5	1	SYNONYMOUS_CODING Ets65A
3L	10934675	3L_10934675_SNP [dm3] 3L_10941575_SNP [dm6]	T	A	6.096e^-5	1	INTERGENIC
3R	6239321	3R_6239321_SNP [dm3] 3R_10413599_SNP [dm6]	C	T	6.134e^-5	1	SYNONYMOUS_CODING Rrp46 UPSTREAM Irp-1B DOWNSTREAM CG6345	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	18592817	2R_18592817_SNP [dm3] 2R_22705312_SNP [dm6]	C	T	6.142e^-5	1	UPSTREAM CG30259 DOWNSTREAM Obp58c INTRON Obp58b
3L	4090499	3L_4090499_SNP [dm3] 3L_4090499_SNP [dm6]	A	G	6.265e^-5	1	SYNONYMOUS_CODING CG14989	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	6791627	3R_6791627_SNP [dm3] 3R_10965905_SNP [dm6]	T	G	6.266e^-5	1	INTERGENIC
2L	12137519	2L_12137519_SNP [dm3] 2L_12137519_SNP [dm6]	T	C	6.276e^-5	1	UPSTREAM Gr33a INTERGENIC
2L	10956638	2L_10956638_SNP [dm3] 2L_10956638_SNP [dm6]	A	G	6.304e^-5	1	INTRON dpr2
3L	4035087	3L_4035087_SNP [dm3] 3L_4035087_SNP [dm6]	A	C	6.314e^-5	1	SYNONYMOUS_CODING Gr64e UTR_3_PRIME Gr64d UPSTREAM CR45042 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
2R	10425822	2R_10425822_SNP [dm3] 2R_14538317_SNP [dm6]	T	C	6.331e^-5	1	INTRON ttv
3L	4035084	3L_4035084_SNP [dm3] 3L_4035084_SNP [dm6]	C	A	6.345e^-5	1	SYNONYMOUS_CODING Gr64e UTR_3_PRIME Gr64d UPSTREAM CR45042 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
2L	9663517	2L_9663517_SNP [dm3] 2L_9663517_SNP [dm6]	C	T	6.378e^-5	1	INTERGENIC
3L	8877086	3L_8877086_SNP [dm3] 3L_8883986_SNP [dm6]	A	C	6.410e^-5	1	INTRON dally
3L	22840756	3L_22840756_DEL [dm3] 3L_22847656_DEL [dm6]	GCCTTTGCTTGAAG...	G	6.443e^-5	1	DOWNSTREAM tRNA:CR32460 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	7963144	2R_7963144_SNP [dm3] 2R_12075639_SNP [dm6]	T	C	6.500e^-5	1	INTRON CG8888
2L	9663345	2L_9663345_INS [dm3] 2L_9663345_INS [dm6]	A	AA	6.518e^-5	1	INTERGENIC
X	10608750	X_10608750_SNP [dm3] X_10714717_SNP [dm6]	G	T	6.616e^-5	1	SYNONYMOUS_CODING CG32676	TF binding site mE1_TFBS_chinmo
3L	8702117	3L_8702117_SNP [dm3] 3L_8709017_SNP [dm6]	C	T	6.618e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3R	11411679	3R_11411679_SNP [dm3] 3R_15585957_SNP [dm6]	A	T	6.706e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Climbing_Control phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results