©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=9.297e-7)
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.
ANOVA test
No significant result.
No significant result.
Kruskal-Wallis test
| Covariate | χ2 | p-value | Significance |
|---|---|---|---|
| In_3R_Mo | 5.7809 | 0.0555 |
GWAS results
1304
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 | |
|---|---|---|---|---|---|---|---|---|---|
| X | 10292788 | X_10292788_SNP [dm3] X_10398755_SNP [dm6] | A | G | 4.802e-6 | 1 |
INTRON
flw |
||
| 2R | 9605748 | 2R_9605748_SNP [dm3] 2R_13718243_SNP [dm6] | C | T | 4.993e-6 | 1 |
INTRON
fas |
||
| 2R | 19363325 | 2R_19363325_SNP [dm3] 2R_23475802_SNP [dm6] | C | T | 1.330e-5 | 1 |
UTR_3_PRIME
CG13557 UPSTREAM CR43792 INTRON CG43795 |
||
| 3L | 9546163 | 3L_9546163_SNP [dm3] 3L_9553063_SNP [dm6] | T | A | 1.351e-5 | 1 |
UTR_5_PRIME
CG42673 |
||
| 3R | 17110098 | 3R_17110098_SNP [dm3] 3R_21284376_SNP [dm6] | A | C | 1.367e-5 | 1 |
DOWNSTREAM
CG17298 INTRON SIFaR |
||
| 2R | 11277421 | 2R_11277421_SNP [dm3] 2R_15389916_SNP [dm6] | C | A | 1.660e-5 | 1 |
INTERGENIC
|
||
| 2L | 9950238 | 2L_9950238_SNP [dm3] 2L_9950238_SNP [dm6] | G | C | 1.749e-5 | 1 |
DOWNSTREAM
mir-87 INTERGENIC |
||
| 3R | 14207821 | 3R_14207821_SNP [dm3] 3R_18382099_SNP [dm6] | T | C | 1.791e-5 | 1 |
SYNONYMOUS_CODING
CG14309 UPSTREAM CG7675 |
TF binding site
mE1_TFBS_cad
|
|
| 2R | 10713687 | 2R_10713687_SNP [dm3] 2R_14826182_SNP [dm6] | G | T | 1.839e-5 | 1 |
INTERGENIC
|
||
| 3L | 7191150 | 3L_7191150_SNP [dm3] 3L_7198050_SNP [dm6] | T | A | 1.989e-5 | 1 |
INTERGENIC
|
||
| 2L | 3975771 | 2L_3975771_SNP [dm3] 2L_3975771_SNP [dm6] | G | A | 2.290e-5 | 1 |
INTRON
fred |
||
| 3R | 14283601 | 3R_14283601_SNP [dm3] 3R_18457879_SNP [dm6] | G | A | 2.452e-5 | 1 |
INTRON
fru |
||
| 2R | 11277411 | 2R_11277411_SNP [dm3] 2R_15389906_SNP [dm6] | A | G | 2.494e-5 | 1 |
INTERGENIC
|
||
| 3R | 26804597 | 3R_26804597_SNP [dm3] 3R_30978875_SNP [dm6] | C | G | 2.571e-5 | 1 |
INTRON
5-HT7 |
||
| 3L | 18629234 | 3L_18629234_SNP [dm3] 3L_18636134_SNP [dm6] | A | C | 2.623e-5 | 1 |
INTRON
MYPT-75D |
||
| 3L | 2510211 | 3L_2510211_SNP [dm3] 3L_2510211_SNP [dm6] | G | A | 2.705e-5 | 1 |
SYNONYMOUS_CODING
Spn INTRON Spn |
TF binding site
mE1_TFBS_chinmo mE1_TFBS_HSA
|
|
| X | 9440402 | X_9440402_SNP [dm3] X_9546369_SNP [dm6] | T | C | 2.853e-5 | 1 |
INTRON
CG32700 |
||
| X | 9440406 | X_9440406_SNP [dm3] X_9546373_SNP [dm6] | A | C | 2.853e-5 | 1 |
INTRON
CG32700 |
||
| 3R | 9423488 | 3R_9423488_SNP [dm3] 3R_13597766_SNP [dm6] | A | C | 2.990e-5 | 1 |
INTERGENIC
|
TF binding site
mE1_TFBS_inv
|
|
| X | 21930245 | X_21930245_SNP [dm3] X_22528409_SNP [dm6] | G | C | 3.011e-5 | 1 |
NON_SYNONYMOUS_CODING
CG17600 |
||
| 3R | 26436194 | 3R_26436194_SNP [dm3] 3R_30610472_SNP [dm6] | T | A | 3.027e-5 | 1 |
DOWNSTREAM
CG31016 INTERGENIC |
||
| 3R | 26436195 | 3R_26436195_SNP [dm3] 3R_30610473_SNP [dm6] | G | T | 3.027e-5 | 1 |
DOWNSTREAM
CG31016 INTERGENIC |
||
| 2R | 18874882 | 2R_18874882_SNP [dm3] 2R_22987359_SNP [dm6] | G | A | 3.069e-5 | 1 |
DOWNSTREAM
CR42742 INTRON twi |
||
| 2L | 8567695 | 2L_8567695_SNP [dm3] 2L_8567695_SNP [dm6] | A | G | 3.613e-5 | 1 |
INTRON
Sema-1a |
||
| 2L | 8567701 | 2L_8567701_SNP [dm3] 2L_8567701_SNP [dm6] | T | C | 3.613e-5 | 1 |
INTRON
Sema-1a |
||
| 2L | 8567709 | 2L_8567709_SNP [dm3] 2L_8567709_SNP [dm6] | A | G | 3.613e-5 | 1 |
INTRON
Sema-1a |
||
| 2L | 8567721 | 2L_8567721_SNP [dm3] 2L_8567721_SNP [dm6] | A | G | 3.613e-5 | 1 |
INTRON
Sema-1a |
||
| X | 17720038 | X_17720038_SNP [dm3] X_17826005_SNP [dm6] | T | A | 4.026e-5 | 1 |
INTRON
Socs16D |
||
| 3L | 19269731 | 3L_19269731_SNP [dm3] 3L_19276631_SNP [dm6] | C | T | 4.238e-5 | 1 |
SYNONYMOUS_CODING
CG14086 |
||
| 2R | 19363037 | 2R_19363037_INS [dm3] 2R_23475514_INS [dm6] | A | AA | 4.355e-5 | 1 |
DOWNSTREAM
CG13557 INTRON CG43795 |
||
| 3R | 17072180 | 3R_17072180_SNP [dm3] 3R_21246458_SNP [dm6] | C | T | 4.443e-5 | 1 |
UPSTREAM
ETHR INTERGENIC |
||
| 3R | 17072347 | 3R_17072347_SNP [dm3] 3R_21246625_SNP [dm6] | C | T | 4.443e-5 | 1 |
UPSTREAM
ETHR INTERGENIC |
||
| 3R | 17072410 | 3R_17072410_SNP [dm3] 3R_21246688_SNP [dm6] | A | T | 4.443e-5 | 1 |
UPSTREAM
ETHR INTERGENIC |
||
| 3R | 17072411 | 3R_17072411_SNP [dm3] 3R_21246689_SNP [dm6] | A | T | 4.443e-5 | 1 |
UPSTREAM
ETHR INTERGENIC |
||
| 2R | 10817872 | 2R_10817872_SNP [dm3] 2R_14930367_SNP [dm6] | T | C | 4.509e-5 | 1 |
SYNONYMOUS_CODING
CG10253 |
TF binding site
mE1_TFBS_HSA mE1_TFBS_inv
|
|
| 3R | 4522635 | 3R_4522635_SNP [dm3] 3R_8696913_SNP [dm6] | G | C | 4.524e-5 | 1 |
INTRON
hb |
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_z mE1_TFBS_Trl |
|
| 3R | 21789536 | 3R_21789536_SNP [dm3] 3R_25963814_SNP [dm6] | T | C | 4.545e-5 | 1 |
INTRON
boss |
||
| 2L | 8567741 | 2L_8567741_SNP [dm3] 2L_8567741_SNP [dm6] | G | T | 4.546e-5 | 1 |
INTRON
Sema-1a |
||
| 2L | 8567742 | 2L_8567742_SNP [dm3] 2L_8567742_SNP [dm6] | C | G | 4.546e-5 | 1 |
INTRON
Sema-1a |
||
| 2L | 4343818 | 2L_4343818_SNP [dm3] 2L_4343818_SNP [dm6] | C | G | 4.667e-5 | 1 |
SYNONYMOUS_CODING
Atet DOWNSTREAM mir-1005 |
TF binding site
mE1_TFBS_inv
|
|
| 2L | 974661 | 2L_974661_SNP [dm3] 2L_974661_SNP [dm6] | G | A | 4.677e-5 | 1 |
INTERGENIC
|
TF binding site
BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_Trl
|
|
| 2R | 12760640 | 2R_12760640_SNP [dm3] 2R_16873135_SNP [dm6] | T | G | 4.773e-5 | 1 |
SYNONYMOUS_CODING
CG6429 UPSTREAM CG6435 DOWNSTREAM CG6421 |
TF binding site
BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
|
|
| X | 21952681 | X_21952681_INS [dm3] X_22550845_INS [dm6] | T | TCGGAATCGGATT... | 4.878e-5 | 1 |
INTERGENIC
|
||
| 2R | 9589938 | 2R_9589938_SNP [dm3] 2R_13702433_SNP [dm6] | A | G | 4.900e-5 | 1 |
INTRON
fas |
||
| 2L | 9212088 | 2L_9212088_SNP [dm3] 2L_9212088_SNP [dm6] | G | A | 5.029e-5 | 1 |
INTRON
tai |
TF binding site
BDTNP1_TFBS_dl
|
|
| 2L | 9212091 | 2L_9212091_SNP [dm3] 2L_9212091_SNP [dm6] | G | A | 5.029e-5 | 1 |
INTRON
tai |
TF binding site
BDTNP1_TFBS_dl
|
|
| X | 21930117 | X_21930117_SNP [dm3] X_22528281_SNP [dm6] | G | C | 5.201e-5 | 1 |
SYNONYMOUS_CODING
CG17600 |
||
| 2L | 4301962 | 2L_4301962_SNP [dm3] 2L_4301962_SNP [dm6] | C | T | 5.217e-5 | 1 |
INTRON
tutl |
TF binding site
BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
|
|
| 2L | 3977222 | 2L_3977222_SNP [dm3] 2L_3977222_SNP [dm6] | T | A | 5.305e-5 | 1 |
INTRON
fred |
||
| 3R | 14283012 | 3R_14283012_SNP [dm3] 3R_18457290_SNP [dm6] | A | G | 5.314e-5 | 1 |
INTRON
fru |
||
| 2R | 9207530 | 2R_9207530_SNP [dm3] 2R_13320025_SNP [dm6] | A | T | 5.376e-5 | 1 |
INTERGENIC
|
TF binding site
mE1_TFBS_inv
|
|
| 3R | 17595350 | 3R_17595350_SNP [dm3] 3R_21769628_SNP [dm6] | T | C | 5.389e-5 | 1 |
SYNONYMOUS_CODING
Burs DOWNSTREAM CG42335 & 1 other |
||
| 2R | 12760623 | 2R_12760623_SNP [dm3] 2R_16873118_SNP [dm6] | T | G | 5.403e-5 | 1 |
NON_SYNONYMOUS_CODING
CG6429 UPSTREAM CG6435 DOWNSTREAM CG6421 |
TF binding site
BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
|
|
| 3L | 2353118 | 3L_2353118_SNP [dm3] 3L_2353118_SNP [dm6] | T | A | 5.521e-5 | 1 |
INTERGENIC
|
||
| 2L | 3974407 | 2L_3974407_DEL [dm3] 2L_3974407_DEL [dm6] | TTTATTT | T | 5.564e-5 | 1 |
INTRON
fred |
||
| 2R | 17323977 | 2R_17323977_SNP [dm3] 2R_21436472_SNP [dm6] | T | G | 5.612e-5 | 1 |
INTRON
Sdc |
||
| 2R | 3732280 | 2R_3732280_SNP [dm3] 2R_7844775_SNP [dm6] | C | T | 5.761e-5 | 1 |
INTRON
Dgk |
||
| 3L | 1473691 | 3L_1473691_SNP [dm3] 3L_1473691_SNP [dm6] | C | A | 5.968e-5 | 1 |
START_GAINED
Ptp61F UTR_5_PRIME Ptp61F |
||
| X | 8293445 | X_8293445_SNP [dm3] X_8399412_SNP [dm6] | G | A | 5.994e-5 | 1 |
SYNONYMOUS_CODING
CG10555 |
TF binding site
BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
|
|
| 2R | 5390505 | 2R_5390505_SNP [dm3] 2R_9503000_SNP [dm6] | C | T | 6.077e-5 | 1 |
SYNONYMOUS_CODING
Wnt2 UPSTREAM brp |
TF binding site
mE1_TFBS_cad
|
|
| 3L | 20100851 | 3L_20100851_SNP [dm3] 3L_20107751_SNP [dm6] | C | T | 6.137e-5 | 1 |
DOWNSTREAM
Ir76b & 1 other INTERGENIC |
TF binding site
BDTNP1_TFBS_dl
transposable element FlyBase |
|
| 2R | 5390475 | 2R_5390475_SNP [dm3] 2R_9502970_SNP [dm6] | A | G | 6.208e-5 | 1 |
SYNONYMOUS_CODING
Wnt2 UPSTREAM brp |
TF binding site
mE1_TFBS_cad
|
|
| 3R | 17110086 | 3R_17110086_SNP [dm3] 3R_21284364_SNP [dm6] | T | C | 6.379e-5 | 1 |
DOWNSTREAM
CG17298 INTRON SIFaR |
||
| 2R | 19575398 | 2R_19575398_SNP [dm3] 2R_23687875_SNP [dm6] | T | C | 6.510e-5 | 1 |
UTR_3_PRIME
St3 UPSTREAM Pal2 |
TF binding site
BDTNP1_TFBS_twi mE1_TFBS_cad
|
|
| 3R | 14283027 | 3R_14283027_DEL [dm3] 3R_18457305_DEL [dm6] | TATAT | T | 6.588e-5 | 1 |
INTRON
fru |
||
| 3L | 11883868 | 3L_11883868_SNP [dm3] 3L_11890768_SNP [dm6] | G | T | 6.736e-5 | 1 |
INTRON
CG44837 |
||
| 2L | 3977220 | 2L_3977220_SNP [dm3] 2L_3977220_SNP [dm6] | T | C | 6.888e-5 | 1 |
INTRON
fred |
||
| X | 18849033 | X_18849033_SNP [dm3] X_18955000_SNP [dm6] | G | A | 6.930e-5 | 1 |
INTRON
CG43759 |
||
| 3R | 24107259 | 3R_24107259_SNP [dm3] 3R_28281537_SNP [dm6] | T | G | 6.947e-5 | 1 |
INTERGENIC
|
||
| 2L | 7505616 | 2L_7505616_SNP [dm3] 2L_7505616_SNP [dm6] | C | G | 6.996e-5 | 1 |
INTRON
RapGAP1 |
TF binding site
mE1_TFBS_bab1 mE1_TFBS_cad
|
|
| 2L | 9150494 | 2L_9150494_SNP [dm3] 2L_9150494_SNP [dm6] | A | G | 7.118e-5 | 1 |
UPSTREAM
CG32982 INTRON CG32982 |
TF binding site
BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
|
|
| 2L | 1873576 | 2L_1873576_SNP [dm3] 2L_1873576_SNP [dm6] | G | C | 7.142e-5 | 1 |
DOWNSTREAM
CR44075 INTRON CG31663 |
||
| 2L | 1873594 | 2L_1873594_SNP [dm3] 2L_1873594_SNP [dm6] | G | C | 7.142e-5 | 1 |
DOWNSTREAM
CR44075 INTRON CG31663 |
||
| 2L | 12234844 | 2L_12234844_SNP [dm3] 2L_12234844_SNP [dm6] | C | G | 7.333e-5 | 1 |
INTRON
aret |
||
| 2L | 12234845 | 2L_12234845_INS [dm3] 2L_12234845_INS [dm6] | G | GAAGTAAAGTACATAA... | 7.333e-5 | 1 |
INTRON
aret |
||
| 2L | 12234848 | 2L_12234848_SNP [dm3] 2L_12234848_SNP [dm6] | A | T | 7.333e-5 | 1 |
INTRON
aret |
||
| 2L | 12234851 | 2L_12234851_INS [dm3] 2L_12234851_INS [dm6] | T | TAAGCTGGGCAGTAACCAAT... | 7.333e-5 | 1 |
INTRON
aret |
||
| 2R | 11277664 | 2R_11277664_SNP [dm3] 2R_15390159_SNP [dm6] | A | T | 7.415e-5 | 1 |
INTERGENIC
|
||
| 3L | 10699624 | 3L_10699624_SNP [dm3] 3L_10706524_SNP [dm6] | A | G | 7.638e-5 | 1 |
INTERGENIC
|
||
| 3L | 10699625 | 3L_10699625_SNP [dm3] 3L_10706525_SNP [dm6] | C | A | 7.638e-5 | 1 |
INTERGENIC
|
||
| 3R | 8706304 | 3R_8706304_SNP [dm3] 3R_12880582_SNP [dm6] | A | G | 7.682e-5 | 1 |
INTERGENIC
|
||
| X | 18472655 | X_18472655_DEL [dm3] X_18578622_DEL [dm6] | CC | C | 7.797e-5 | 1 |
INTERGENIC
|
||
| 2R | 13491426 | 2R_13491426_SNP [dm3] 2R_17603921_SNP [dm6] | A | T | 7.806e-5 | 1 |
UTR_3_PRIME
lack UPSTREAM tRNA:CR30231 DOWNSTREAM tRNA:CR30333 |
||
| 3R | 14499179 | 3R_14499179_SNP [dm3] 3R_18673457_SNP [dm6] | G | A | 7.843e-5 | 1 |
SYNONYMOUS_CODING
CG7702 |
TF binding site
mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
|
|
| 3R | 14284065 | 3R_14284065_SNP [dm3] 3R_18458343_SNP [dm6] | G | C | 7.847e-5 | 1 |
INTRON
fru |
||
| 3L | 14165617 | 3L_14165617_SNP [dm3] 3L_14172517_SNP [dm6] | T | A | 7.899e-5 | 1 |
INTERGENIC
|
regulatory region
REDfly_CRMs
TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad |
|
| 2R | 5513921 | 2R_5513921_DEL [dm3] 2R_9626416_DEL [dm6] | TGTTTGTGTGT... | T | 8.023e-5 | 1 |
INTRON
Mmp2 |
||
| 2L | 9687822 | 2L_9687822_SNP [dm3] 2L_9687822_SNP [dm6] | A | T | 8.064e-5 | 1 |
INTRON
Pka-C1 |
||
| X | 10292802 | X_10292802_INS [dm3] X_10398769_INS [dm6] | C | CC | 8.167e-5 | 1 |
INTRON
flw |
||
| 3L | 4112140 | 3L_4112140_SNP [dm3] 3L_4112140_SNP [dm6] | A | G | 8.196e-5 | 1 |
SYNONYMOUS_CODING
Ack |
TF binding site
mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
|
|
| 3R | 17666338 | 3R_17666338_SNP [dm3] 3R_21840616_SNP [dm6] | T | A | 8.302e-5 | 1 |
INTERGENIC
|
||
| 3L | 13470026 | 3L_13470026_SNP [dm3] 3L_13476926_SNP [dm6] | A | T | 8.353e-5 | 1 |
UPSTREAM
stv INTERGENIC |
TF binding site
BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
|
|
| 3L | 13470036 | 3L_13470036_SNP [dm3] 3L_13476936_SNP [dm6] | A | G | 8.353e-5 | 1 |
UPSTREAM
stv INTERGENIC |
TF binding site
BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
|
|
| 2L | 3259769 | 2L_3259769_SNP [dm3] 2L_3259769_SNP [dm6] | T | C | 8.393e-5 | 1 |
INTERGENIC
|
||
| 2L | 9513717 | 2L_9513717_SNP [dm3] 2L_9513717_SNP [dm6] | A | G | 8.752e-5 | 1 |
INTRON
CG33298 |
||
| X | 18349164 | X_18349164_SNP [dm3] X_18455131_SNP [dm6] | T | A | 8.801e-5 | 1 |
INTRON
CG32547 |
||
| 2R | 19365662 | 2R_19365662_SNP [dm3] 2R_23478139_SNP [dm6] | C | A | 8.992e-5 | 1 |
UPSTREAM
CR43793 INTRON CG43795 |
||
| 3R | 19423288 | 3R_19423288_SNP [dm3] 3R_23597566_SNP [dm6] | G | A | 9.189e-5 | 1 |
INTRON
CG10183 |
||
| 3R | 19423291 | 3R_19423291_SNP [dm3] 3R_23597569_SNP [dm6] | G | A | 9.189e-5 | 1 |
INTRON
CG10183 |
||
| 2R | 19372948 | 2R_19372948_SNP [dm3] 2R_23485425_SNP [dm6] | C | T | 9.214e-5 | 1 |
INTRON
CG43795 |
Showing 1 to 100 of 1,000 entries
Missing results