©2022-2025 Deplancke lab, EPFL, 1015 Lausanne
Filters
| By genomic position | |
| Variant impact | |
| Gene name |
| Involved in binding site | |
| Binding site |
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
Phenotype distribution and association to known covariates
Shapiro-Wilk test of normality (p-value=3.221e-3)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype
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.
GWAS results
1653
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
| Chromosome | Position | ID | Reference | Variant | p-value | FDR_BH | Transcript annotation | Binding site annotation | |
|---|---|---|---|---|---|---|---|---|---|
| 3R | 12376242 | 3R_12376242_SNP [dm3] 3R_16550520_SNP [dm6] | C | T | 6.787e-7 | 1 |
INTRON
CG42342 |
TF binding site
BDTNP1_TFBS_da mE1_TFBS_cad
|
|
| 3R | 14771141 | 3R_14771141_SNP [dm3] 3R_18945419_SNP [dm6] | G | C | 1.333e-6 | 1 |
INTRON
CG42613 |
||
| 2R | 6887180 | 2R_6887180_SNP [dm3] 2R_10999675_SNP [dm6] | T | C | 2.681e-6 | 1 |
INTRON
luna |
||
| 3L | 5575742 | 3L_5575742_SNP [dm3] 3L_5582642_SNP [dm6] | G | A | 3.955e-6 | 1 |
INTERGENIC
|
TF binding site
BDTNP1_TFBS_dl
|
|
| 2L | 4767385 | 2L_4767385_SNP [dm3] 2L_4767385_SNP [dm6] | C | G | 4.219e-6 | 1 |
INTRON
CG15630 |
||
| X | 8429900 | X_8429900_SNP [dm3] X_8535867_SNP [dm6] | G | C | 5.273e-6 | 1 |
INTRON
Nrg |
||
| 3R | 13414957 | 3R_13414957_SNP [dm3] 3R_17589235_SNP [dm6] | C | A | 5.753e-6 | 1 |
INTERGENIC
|
TF binding site
BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
|
|
| 2R | 19112174 | 2R_19112174_SNP [dm3] 2R_23224651_SNP [dm6] | G | T | 8.435e-6 | 1 |
INTERGENIC
|
||
| 3R | 13414963 | 3R_13414963_SNP [dm3] 3R_17589241_SNP [dm6] | G | C | 9.290e-6 | 1 |
INTERGENIC
|
TF binding site
BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
|
|
| 3R | 12215625 | 3R_12215625_SNP [dm3] 3R_16389903_SNP [dm6] | A | G | 9.834e-6 | 1 |
INTRON
ss |
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA |
|
| 3L | 9837314 | 3L_9837314_SNP [dm3] 3L_9844214_SNP [dm6] | G | A | 1.175e-5 | 1 |
SYNONYMOUS_CODING
RasGAP1 |
TF binding site
BDTNP1_TFBS_Mad mE1_TFBS_HSA
|
|
| 3R | 25996118 | 3R_25996118_SNP [dm3] 3R_30170396_SNP [dm6] | C | T | 1.389e-5 | 1 |
SYNONYMOUS_CODING
CG31028 |
||
| 2R | 6887471 | 2R_6887471_SNP [dm3] 2R_10999966_SNP [dm6] | A | C | 1.614e-5 | 1 |
INTRON
luna |
||
| 3R | 11952988 | 3R_11952988_INS [dm3] 3R_16127266_INS [dm6] | T | TCATTCTTAAGAACAACTTT... | 1.783e-5 | 1 |
INTRON
Sb |
||
| 2L | 10711452 | 2L_10711452_SNP [dm3] 2L_10711452_SNP [dm6] | C | T | 1.800e-5 | 1 |
DOWNSTREAM
CR44407 INTERGENIC |
||
| 2R | 16752621 | 2R_16752621_SNP [dm3] 2R_20865116_SNP [dm6] | G | T | 1.869e-5 | 1 |
INTRON
CG15227 |
||
| 3L | 1411752 | 3L_1411752_SNP [dm3] 3L_1411752_SNP [dm6] | A | T | 2.102e-5 | 1 |
SYNONYMOUS_CODING
CG9168 INTRON Ptp61F |
TF binding site
mE1_TFBS_sens
|
|
| X | 19689391 | X_19689391_SNP [dm3] X_19795358_SNP [dm6] | A | T | 2.139e-5 | 1 |
INTERGENIC
|
||
| 2R | 6132264 | 2R_6132264_DEL [dm3] 2R_10244759_DEL [dm6] | AT | A | 2.208e-5 | 1 |
INTRON
Hdc |
||
| 3R | 3895165 | 3R_3895165_SNP [dm3] 3R_8069443_SNP [dm6] | G | A | 2.228e-5 | 1 |
INTRON
mAChR-B |
||
| 2L | 14010939 | 2L_14010939_SNP [dm3] 2L_14010939_SNP [dm6] | C | T | 2.265e-5 | 1 |
UPSTREAM
tRNA:Q:34E INTERGENIC |
||
| 3R | 2359077 | 3R_2359077_SNP [dm3] 3R_6533355_SNP [dm6] | G | C | 2.308e-5 | 1 |
INTRON
dpr11 |
||
| 3L | 2525375 | 3L_2525375_SNP [dm3] 3L_2525375_SNP [dm6] | C | T | 2.355e-5 | 1 |
SYNONYMOUS_CODING
Spn DOWNSTREAM CG32295 |
TF binding site
BDTNP1_TFBS_sna mE1_TFBS_HSA
|
|
| 2R | 10707643 | 2R_10707643_SNP [dm3] 2R_14820138_SNP [dm6] | T | G | 2.460e-5 | 1 |
UPSTREAM
CG10202 INTERGENIC |
||
| 3R | 24579408 | 3R_24579408_SNP [dm3] 3R_28753686_SNP [dm6] | T | C | 2.473e-5 | 1 |
INTERGENIC
|
||
| 2L | 5135959 | 2L_5135959_SNP [dm3] 2L_5135959_SNP [dm6] | C | G | 2.557e-5 | 1 |
NON_SYNONYMOUS_CODING
Msp300 INTRON Msp300 |
||
| 2L | 19629965 | 2L_19629965_SNP [dm3] 2L_19629965_SNP [dm6] | T | A | 2.612e-5 | 1 |
INTRON
Lar |
||
| 3L | 19090631 | 3L_19090631_SNP [dm3] 3L_19097531_SNP [dm6] | G | A | 2.676e-5 | 1 |
SYNONYMOUS_CODING
CG10424 UPSTREAM CG14079 |
TF binding site
mE1_TFBS_cad
|
|
| X | 12027348 | X_12027348_SNP [dm3] X_12133315_SNP [dm6] | T | C | 2.729e-5 | 1 |
INTRON
Ten-a |
||
| 2R | 19112207 | 2R_19112207_SNP [dm3] 2R_23224684_SNP [dm6] | T | C | 2.855e-5 | 1 |
INTERGENIC
|
||
| 3R | 22761028 | 3R_22761028_SNP [dm3] 3R_26935306_SNP [dm6] | T | G | 2.874e-5 | 1 |
INTRON
sda |
||
| 3R | 26678179 | 3R_26678179_SNP [dm3] 3R_30852457_SNP [dm6] | A | G | 2.885e-5 | 1 |
UTR_5_PRIME
tll |
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl |
|
| 2R | 1186717 | 2R_1186717_SNP [dm3] 2R_5299212_SNP [dm6] | T | G | 2.980e-5 | 1 |
INTERGENIC
|
||
| 2L | 14008707 | 2L_14008707_SNP [dm3] 2L_14008707_SNP [dm6] | A | T | 3.052e-5 | 1 |
UTR_3_PRIME
CG42692 |
||
| 3R | 23982674 | 3R_23982674_SNP [dm3] 3R_28156952_SNP [dm6] | T | G | 3.205e-5 | 1 |
INTRON
CG34354 |
||
| 3R | 14771158 | 3R_14771158_SNP [dm3] 3R_18945436_SNP [dm6] | G | A | 3.253e-5 | 1 |
INTRON
CG42613 |
||
| 2R | 1179199 | 2R_1179199_SNP [dm3] 2R_5291694_SNP [dm6] | C | A | 3.393e-5 | 1 |
INTRON
d4 |
transposable element
FlyBase
|
|
| 2R | 19112146 | 2R_19112146_SNP [dm3] 2R_23224623_SNP [dm6] | G | C | 3.620e-5 | 1 |
INTERGENIC
|
||
| 2R | 19112150 | 2R_19112150_SNP [dm3] 2R_23224627_SNP [dm6] | G | C | 3.620e-5 | 1 |
INTERGENIC
|
||
| 2L | 12781135 | 2L_12781135_SNP [dm3] 2L_12781135_SNP [dm6] | G | T | 3.665e-5 | 1 |
INTERGENIC
|
||
| 2L | 6304002 | 2L_6304002_SNP [dm3] 2L_6304002_SNP [dm6] | C | T | 3.742e-5 | 1 |
INTRON
Ddr |
||
| X | 20705911 | X_20705911_SNP [dm3] X_20834884_SNP [dm6] | A | G | 4.017e-5 | 1 |
INTRON
shakB |
||
| 2L | 6626194 | 2L_6626194_SNP [dm3] 2L_6626194_SNP [dm6] | G | C | 4.098e-5 | 1 |
NON_SYNONYMOUS_CODING
Oatp26F DOWNSTREAM CG34345 |
TF binding site
BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
|
|
| 3R | 24307840 | 3R_24307840_SNP [dm3] 3R_28482118_SNP [dm6] | C | T | 4.118e-5 | 1 |
INTERGENIC
|
||
| 2R | 12136512 | 2R_12136512_SNP [dm3] 2R_16249007_SNP [dm6] | G | T | 4.257e-5 | 1 |
INTRON
CngA |
||
| 2R | 9873228 | 2R_9873228_SNP [dm3] 2R_13985723_SNP [dm6] | T | A | 4.291e-5 | 1 |
SYNONYMOUS_CODING
RN-tre UTR_3_PRIME RN-tre DOWNSTREAM CG8067 & 1 other |
||
| X | 20688576 | X_20688576_SNP [dm3] X_20817549_SNP [dm6] | A | C | 4.370e-5 | 1 |
INTRON
shakB |
||
| X | 2889174 | X_2889174_DEL [dm3] X_2995141_DEL [dm6] | GGG | G | 4.502e-5 | 1 |
UTR_5_PRIME
kirre |
||
| 3R | 9900042 | 3R_9900042_SNP [dm3] 3R_14074320_SNP [dm6] | C | T | 4.565e-5 | 1 |
INTRON
foxo |
||
| 3L | 2525372 | 3L_2525372_SNP [dm3] 3L_2525372_SNP [dm6] | T | C | 4.641e-5 | 1 |
SYNONYMOUS_CODING
Spn DOWNSTREAM CG32295 |
TF binding site
BDTNP1_TFBS_sna mE1_TFBS_HSA
|
|
| 3L | 12630613 | 3L_12630613_SNP [dm3] 3L_12637513_SNP [dm6] | T | C | 4.867e-5 | 1 |
INTRON
CR32111 |
||
| 3R | 23927184 | 3R_23927184_SNP [dm3] 3R_28101462_SNP [dm6] | C | T | 4.879e-5 | 1 |
INTERGENIC
|
||
| 3L | 7801328 | 3L_7801328_SNP [dm3] 3L_7808228_SNP [dm6] | G | T | 5.000e-5 | 1 |
INTRON
CG32369 |
TF binding site
mE1_TFBS_Trl
|
|
| 3L | 1062877 | 3L_1062877_SNP [dm3] 3L_1062877_SNP [dm6] | G | C | 5.112e-5 | 1 |
INTRON
bab1 |
||
| 3L | 11766632 | 3L_11766632_SNP [dm3] 3L_11773532_SNP [dm6] | C | A | 5.126e-5 | 1 |
DOWNSTREAM
mir-956 & 2 others INTERGENIC |
||
| 3L | 3630474 | 3L_3630474_SNP [dm3] 3L_3630474_SNP [dm6] | C | G | 5.202e-5 | 1 |
INTRON
dar1 |
||
| 3R | 24952794 | 3R_24952794_SNP [dm3] 3R_29127072_SNP [dm6] | T | C | 5.219e-5 | 1 |
SYNONYMOUS_CODING
CG11880 |
TF binding site
mE1_TFBS_cad mE1_TFBS_HSA
|
|
| 3L | 11756279 | 3L_11756279_SNP [dm3] 3L_11763179_SNP [dm6] | G | C | 5.487e-5 | 1 |
INTRON
CG6024 |
||
| 3R | 23841932 | 3R_23841932_SNP [dm3] 3R_28016210_SNP [dm6] | A | G | 6.024e-5 | 1 |
INTERGENIC
|
||
| 2R | 6336235 | 2R_6336235_SNP [dm3] 2R_10448730_SNP [dm6] | T | C | 6.055e-5 | 1 |
DOWNSTREAM
Cyp49a1 INTRON Galphao |
||
| 3R | 12232683 | 3R_12232683_SNP [dm3] 3R_16406961_SNP [dm6] | A | C | 6.085e-5 | 1 |
EXON
CR45630 |
||
| 3R | 12376218 | 3R_12376218_SNP [dm3] 3R_16550496_SNP [dm6] | G | C | 6.113e-5 | 1 |
INTRON
CG42342 |
TF binding site
BDTNP1_TFBS_da
|
|
| X | 2690753 | X_2690753_INS [dm3] X_2796720_INS [dm6] | A | ACAAAT | 6.130e-5 | 1 |
UPSTREAM
w INTRON kirre |
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA |
|
| 3L | 11582640 | 3L_11582640_SNP [dm3] 3L_11589540_SNP [dm6] | T | A | 6.163e-5 | 1 |
UPSTREAM
CG7377 INTERGENIC |
||
| 2R | 11590337 | 2R_11590337_SNP [dm3] 2R_15702832_SNP [dm6] | G | T | 6.250e-5 | 1 |
INTERGENIC
|
TF binding site
BDTNP1_TFBS_twi
|
|
| 3L | 7801293 | 3L_7801293_SNP [dm3] 3L_7808193_SNP [dm6] | G | A | 6.322e-5 | 1 |
INTRON
CG32369 |
TF binding site
mE1_TFBS_Trl
|
|
| 2L | 5624367 | 2L_5624367_SNP [dm3] 2L_5624367_SNP [dm6] | C | A | 6.347e-5 | 1 |
UPSTREAM
Cyp6a16 INTERGENIC |
TF binding site
mE1_TFBS_bab1
|
|
| 3R | 14771185 | 3R_14771185_INS [dm3] 3R_18945463_INS [dm6] | A | AAAAGA | 6.352e-5 | 1 |
INTRON
CG42613 |
||
| 2L | 12781139 | 2L_12781139_SNP [dm3] 2L_12781139_SNP [dm6] | T | G | 6.413e-5 | 1 |
INTERGENIC
|
||
| 2L | 16078891 | 2L_16078891_SNP [dm3] 2L_16078891_SNP [dm6] | A | C | 6.486e-5 | 1 |
INTRON
beat-Ia |
||
| 2R | 1089662 | 2R_1089662_SNP [dm3] 2R_5202157_SNP [dm6] | A | G | 6.514e-5 | 1 |
INTRON
Nipped-A |
||
| 2L | 12781172 | 2L_12781172_SNP [dm3] 2L_12781172_SNP [dm6] | A | T | 6.555e-5 | 1 |
INTERGENIC
|
||
| 2R | 14343546 | 2R_14343546_SNP [dm3] 2R_18456041_SNP [dm6] | G | T | 6.683e-5 | 1 |
DOWNSTREAM
CG30116 INTERGENIC |
||
| 2L | 14008823 | 2L_14008823_SNP [dm3] 2L_14008823_SNP [dm6] | A | T | 6.906e-5 | 1 |
DOWNSTREAM
CG42692 INTERGENIC |
||
| 2R | 12436655 | 2R_12436655_SNP [dm3] 2R_16549150_SNP [dm6] | T | A | 6.961e-5 | 1 |
INTERGENIC
|
||
| 3R | 3623262 | 3R_3623262_SNP [dm3] 3R_7797540_SNP [dm6] | C | T | 7.126e-5 | 1 |
SYNONYMOUS_CODING
CG18744 DOWNSTREAM CG2641 |
||
| 2R | 14151354 | 2R_14151354_SNP [dm3] 2R_18263849_SNP [dm6] | G | T | 7.158e-5 | 1 |
INTERGENIC
|
||
| 2L | 10053577 | 2L_10053577_SNP [dm3] 2L_10053577_SNP [dm6] | C | A | 7.197e-5 | 1 |
UPSTREAM
CR44875 & 1 other INTERGENIC |
||
| 2L | 10053578 | 2L_10053578_SNP [dm3] 2L_10053578_SNP [dm6] | C | T | 7.197e-5 | 1 |
UPSTREAM
CR44875 & 1 other INTERGENIC |
||
| X | 11899055 | X_11899055_SNP [dm3] X_12005022_SNP [dm6] | C | T | 7.381e-5 | 1 |
INTERGENIC
|
TF binding site
mE1_TFBS_HSA
|
|
| 2L | 14010952 | 2L_14010952_SNP [dm3] 2L_14010952_SNP [dm6] | T | C | 7.390e-5 | 1 |
UPSTREAM
tRNA:Q:34E INTERGENIC |
||
| X | 2889171 | X_2889171_INS [dm3] X_2995138_INS [dm6] | A | AC | 7.425e-5 | 1 |
UTR_5_PRIME
kirre |
||
| 2L | 12781136 | 2L_12781136_SNP [dm3] 2L_12781136_SNP [dm6] | A | G | 7.474e-5 | 1 |
INTERGENIC
|
||
| 2R | 12136518 | 2R_12136518_SNP [dm3] 2R_16249013_SNP [dm6] | T | C | 7.487e-5 | 1 |
INTRON
CngA |
||
| 2R | 12136520 | 2R_12136520_SNP [dm3] 2R_16249015_SNP [dm6] | G | A | 7.487e-5 | 1 |
INTRON
CngA |
||
| 2R | 15182533 | 2R_15182533_SNP [dm3] 2R_19295028_SNP [dm6] | C | T | 7.572e-5 | 1 |
INTRON
Tab2 |
TF binding site
BDTNP1_TFBS_dl BDTNP1_TFBS_twi
|
|
| 2L | 391220 | 2L_391220_SNP [dm3] 2L_391220_SNP [dm6] | A | T | 7.612e-5 | 1 |
INTERGENIC
|
||
| 3L | 7109947 | 3L_7109947_SNP [dm3] 3L_7116847_SNP [dm6] | A | G | 7.634e-5 | 1 |
INTRON
form3 |
||
| 2R | 12136546 | 2R_12136546_SNP [dm3] 2R_16249041_SNP [dm6] | T | A | 7.704e-5 | 1 |
INTRON
CngA |
||
| 3R | 16506815 | 3R_16506815_SNP [dm3] 3R_20681093_SNP [dm6] | A | C | 7.777e-5 | 1 |
INTERGENIC
|
||
| 3L | 11591114 | 3L_11591114_SNP [dm3] 3L_11598014_SNP [dm6] | T | C | 7.988e-5 | 1 |
INTRON
CG7368 |
TF binding site
mE1_TFBS_cad
|
|
| 3R | 25231389 | 3R_25231389_SNP [dm3] 3R_29405667_SNP [dm6] | G | A | 8.046e-5 | 1 |
INTRON
Ptp99A |
TF binding site
mE1_TFBS_inv
|
|
| 2R | 5384879 | 2R_5384879_SNP [dm3] 2R_9497374_SNP [dm6] | A | T | 8.070e-5 | 1 |
INTRON
Wnt2 |
TF binding site
mE1_TFBS_chinmo mE1_TFBS_HSA
|
|
| 3R | 14771213 | 3R_14771213_SNP [dm3] 3R_18945491_SNP [dm6] | A | C | 8.103e-5 | 1 |
INTRON
CG42613 |
||
| X | 20687181 | X_20687181_SNP [dm3] X_20816154_SNP [dm6] | A | C | 8.551e-5 | 1 |
INTRON
shakB |
||
| 3R | 26678197 | 3R_26678197_SNP [dm3] 3R_30852475_SNP [dm6] | A | T | 8.573e-5 | 1 |
UTR_5_PRIME
tll |
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl |
|
| 2R | 12063295 | 2R_12063295_SNP [dm3] 2R_16175790_SNP [dm6] | C | T | 8.602e-5 | 1 |
SYNONYMOUS_CODING
Ptp52F |
TF binding site
mE1_TFBS_cad
|
|
| 2R | 16321230 | 2R_16321230_SNP [dm3] 2R_20433725_SNP [dm6] | G | A | 8.823e-5 | 1 |
INTRON
CG12484 |
||
| 2L | 9666376 | 2L_9666376_SNP [dm3] 2L_9666376_SNP [dm6] | A | G | 8.879e-5 | 1 |
INTERGENIC
|
||
| 2L | 22102491 | 2L_22102491_SNP [dm3] 2L_22102491_SNP [dm6] | A | G | 8.886e-5 | 1 |
DOWNSTREAM
CG31703 INTERGENIC |
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