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=7.397e^-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

Covariate	p-value	Significance
In_2L_t	0.06554

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	4.4721	0.0345
In_2L_t	6.2315	0.0443

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2387 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
3L	3949365	3L_3949365_SNP [dm3] 3L_3949365_SNP [dm6]	T	C	5.495e^-7	0.448	UPSTREAM CG14983 DOWNSTREAM CG10853 INTERGENIC
3R	4370437	3R_4370437_SNP [dm3] 3R_8544715_SNP [dm6]	T	C	5.910e^-7	0.448	UPSTREAM CR45575 INTERGENIC
3L	6131752	3L_6131752_SNP [dm3] 3L_6138652_SNP [dm6]	A	G	8.919e^-7	0.448	UPSTREAM Lcp65Ae DOWNSTREAM Cpr65Av INTERGENIC
3L	17771268	3L_17771268_SNP [dm3] 3L_17778168_SNP [dm6]	G	T	9.992e^-7	0.448	INTERGENIC
2R	17648180	2R_17648180_SNP [dm3] 2R_21760675_SNP [dm6]	A	T	1.194e^-6	0.448	INTERGENIC
3R	15277868	3R_15277868_SNP [dm3] 3R_19452146_SNP [dm6]	C	A	1.486e^-6	0.464	INTRON CG31221
2R	7888199	2R_7888199_DEL [dm3] 2R_12000694_DEL [dm6]	GAGCCTTTG	G	2.846e^-6	0.639	DOWNSTREAM otk INTERGENIC
2R	16566918	2R_16566918_SNP [dm3] 2R_20679413_SNP [dm6]	C	T	3.118e^-6	0.639	INTERGENIC
3L	3792824	3L_3792824_SNP [dm3] 3L_3792824_SNP [dm6]	C	A	3.995e^-6	0.639	INTRON CG32264
3L	17771270	3L_17771270_SNP [dm3] 3L_17778170_SNP [dm6]	G	A	5.359e^-6	0.639	INTERGENIC
3R	4635583	3R_4635583_SNP [dm3] 3R_8809861_SNP [dm6]	C	T	5.786e^-6	0.639	UPSTREAM CG9837 INTRON CG9837	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_sens
3R	4370439	3R_4370439_SNP [dm3] 3R_8544717_SNP [dm6]	T	G	5.896e^-6	0.639	UPSTREAM CR45575 INTERGENIC
X	15249529	X_15249529_INS [dm3] X_15355496_INS [dm6]	T	TGGCAGCTTT	6.340e^-6	0.639	INTRON acj6	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl
3L	5485885	3L_5485885_SNP [dm3] 3L_5492785_SNP [dm6]	C	T	6.608e^-6	0.639	DOWNSTREAM CR44520 INTERGENIC
3R	23893375	3R_23893375_SNP [dm3] 3R_28067653_SNP [dm6]	G	A	7.429e^-6	0.639	INTRON CG34362
3R	13202531	3R_13202531_SNP [dm3] 3R_17376809_SNP [dm6]	C	T	7.519e^-6	0.639	INTRON Brf
3R	15278013	3R_15278013_SNP [dm3] 3R_19452291_SNP [dm6]	G	A	7.938e^-6	0.639	INTRON CG31221	TF binding site mE1_TFBS_Kr
3L	9691675	3L_9691675_SNP [dm3] 3L_9698575_SNP [dm6]	A	G	8.170e^-6	0.639	UTR_5_PRIME UbcD4	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3794031	3L_3794031_SNP [dm3] 3L_3794031_SNP [dm6]	C	T	8.405e^-6	0.639	INTRON CG32264
3L	17771230	3L_17771230_SNP [dm3] 3L_17778130_SNP [dm6]	G	C	8.701e^-6	0.639	INTERGENIC
2L	6741569	2L_6741569_SNP [dm3] 2L_6741569_SNP [dm6]	A	G	9.487e^-6	0.639	UPSTREAM CG11221 INTERGENIC
3L	3951520	3L_3951520_SNP [dm3] 3L_3951520_SNP [dm6]	G	A	9.547e^-6	0.639	INTRON CG14984
2L	5890114	2L_5890114_SNP [dm3] 2L_5890114_SNP [dm6]	C	T	9.652e^-6	0.639	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16416266	X_16416266_SNP [dm3] X_16522233_SNP [dm6]	T	G	9.689e^-6	0.639	DOWNSTREAM Cnx14D INTRON para
3L	9667834	3L_9667834_SNP [dm3] 3L_9674734_SNP [dm6]	T	C	9.956e^-6	0.639	INTRON fry
3R	26301349	3R_26301349_SNP [dm3] 3R_30475627_SNP [dm6]	A	G	1.011e^-5	0.639	INTRON PH4alphaEFB	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2L	6771751	2L_6771751_SNP [dm3] 2L_6771751_SNP [dm6]	C	T	1.017e^-5	0.639	UPSTREAM CG11321 INTRON CG11321
3L	5377811	3L_5377811_SNP [dm3] 3L_5384711_SNP [dm6]	T	A	1.029e^-5	0.639	INTERGENIC
3R	15278014	3R_15278014_SNP [dm3] 3R_19452292_SNP [dm6]	G	T	1.049e^-5	0.639	INTRON CG31221	TF binding site mE1_TFBS_Kr
X	20453090	X_20453090_INS [dm3] X_20582063_INS [dm6]	G	GCGGTGGCTTGGTG...	1.072e^-5	0.639	INTERGENIC
3L	18956902	3L_18956902_SNP [dm3] 3L_18963802_SNP [dm6]	A	G	1.117e^-5	0.639	INTERGENIC
3R	15024951	3R_15024951_SNP [dm3] 3R_19199229_SNP [dm6]	C	T	1.123e^-5	0.639	INTRON CG31475
2L	6771755	2L_6771755_SNP [dm3] 2L_6771755_SNP [dm6]	A	T	1.149e^-5	0.639	UPSTREAM CG11321 INTRON CG11321
3R	4395482	3R_4395482_SNP [dm3] 3R_8569760_SNP [dm6]	T	C	1.182e^-5	0.639	DOWNSTREAM Cenp-C INTERGENIC
3L	3686501	3L_3686501_SNP [dm3] 3L_3686501_SNP [dm6]	C	T	1.193e^-5	0.639	INTERGENIC
X	15414300	X_15414300_SNP [dm3] X_15520267_SNP [dm6]	A	T	1.306e^-5	0.642	INTRON Ac13E
3L	6975633	3L_6975633_SNP [dm3] 3L_6982533_SNP [dm6]	C	T	1.363e^-5	0.642	DOWNSTREAM CG32388 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	4383673	3R_4383673_SNP [dm3] 3R_8557951_SNP [dm6]	C	A	1.393e^-5	0.642	INTERGENIC
3L	17771337	3L_17771337_SNP [dm3] 3L_17778237_SNP [dm6]	T	A	1.434e^-5	0.642	INTERGENIC
3R	4404266	3R_4404266_SNP [dm3] 3R_8578544_SNP [dm6]	G	A	1.437e^-5	0.642	INTRON 5-HT2B
3L	2803748	3L_2803748_SNP [dm3] 3L_2803748_SNP [dm6]	G	A	1.472e^-5	0.642	INTRON CG43444
3L	3797201	3L_3797201_SNP [dm3] 3L_3797201_SNP [dm6]	A	C	1.477e^-5	0.642	INTRON CG32264
X	16298234	X_16298234_SNP [dm3] X_16404201_SNP [dm6]	T	A	1.562e^-5	0.642	UPSTREAM CG9981 INTRON CG9981
3R	23870290	3R_23870290_SNP [dm3] 3R_28044568_SNP [dm6]	G	T	1.592e^-5	0.642	INTRON CG34362
2L	5890101	2L_5890101_SNP [dm3] 2L_5890101_SNP [dm6]	G	A	1.645e^-5	0.642	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5890104	2L_5890104_SNP [dm3] 2L_5890104_SNP [dm6]	T	C	1.645e^-5	0.642	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17771241	3L_17771241_SNP [dm3] 3L_17778141_SNP [dm6]	C	T	1.732e^-5	0.642	INTERGENIC
2L	7012115	2L_7012115_SNP [dm3] 2L_7012115_SNP [dm6]	T	C	1.790e^-5	0.642	UPSTREAM CG43321 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	17771226	3L_17771226_SNP [dm3] 3L_17778126_SNP [dm6]	A	G	1.855e^-5	0.642	INTERGENIC
3L	3792814	3L_3792814_SNP [dm3] 3L_3792814_SNP [dm6]	G	A	1.945e^-5	0.642	INTRON CG32264
3L	23078553	3L_23078553_DEL [dm3] 3L_23085453_DEL [dm6]	TT	T	1.951e^-5	0.642	INTERGENIC	transposable element FlyBase
3L	17771253	3L_17771253_SNP [dm3] 3L_17778153_SNP [dm6]	A	T	1.952e^-5	0.642	INTERGENIC
3R	12109560	3R_12109560_SNP [dm3] 3R_16283838_SNP [dm6]	C	A	1.979e^-5	0.642	INTRON gish
X	4106661	X_4106661_SNP [dm3] X_4212628_SNP [dm6]	C	T	2.030e^-5	0.642	UPSTREAM CG43288 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	16566909	2R_16566909_SNP [dm3] 2R_20679404_SNP [dm6]	T	C	2.078e^-5	0.642	INTERGENIC
3R	12110205	3R_12110205_SNP [dm3] 3R_16284483_SNP [dm6]	T	C	2.121e^-5	0.642	INTRON gish	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	9057775	2R_9057775_SNP [dm3] 2R_13170270_SNP [dm6]	T	C	2.159e^-5	0.642	INTRON CR45142 & 1 other
3R	26301379	3R_26301379_SNP [dm3] 3R_30475657_SNP [dm6]	T	C	2.178e^-5	0.642	INTRON PH4alphaEFB	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3R	12106887	3R_12106887_SNP [dm3] 3R_16281165_SNP [dm6]	C	A	2.215e^-5	0.642	INTRON gish	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	17771247	3L_17771247_SNP [dm3] 3L_17778147_SNP [dm6]	C	T	2.222e^-5	0.642	INTERGENIC
3L	9693583	3L_9693583_SNP [dm3] 3L_9700483_SNP [dm6]	C	T	2.279e^-5	0.642	DOWNSTREAM CG6761 & 1 other INTERGENIC
X	5073522	X_5073522_SNP [dm3] X_5179489_SNP [dm6]	G	A	2.307e^-5	0.642	DOWNSTREAM CG5062 INTRON rg & 1 other	TF binding site BDTNP1_TFBS_dl
2R	17648177	2R_17648177_SNP [dm3] 2R_21760672_SNP [dm6]	C	A	2.312e^-5	0.642	INTERGENIC
2L	4333914	2L_4333914_SNP [dm3] 2L_4333914_SNP [dm6]	C	T	2.336e^-5	0.642	UTR_5_PRIME Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_zfh1
3L	4782350	3L_4782350_SNP [dm3] 3L_4782350_SNP [dm6]	C	T	2.342e^-5	0.642	INTRON RhoGEF64C
3R	13202558	3R_13202558_SNP [dm3] 3R_17376836_SNP [dm6]	T	C	2.361e^-5	0.642	SYNONYMOUS_CODING Brf
2R	9015023	2R_9015023_SNP [dm3] 2R_13127518_SNP [dm6]	G	C	2.367e^-5	0.642	DOWNSTREAM CG3955 INTERGENIC
2L	9413708	2L_9413708_SNP [dm3] 2L_9413708_SNP [dm6]	C	A	2.374e^-5	0.642	INTRON Shawl
X	12263539	X_12263539_SNP [dm3] X_12369506_SNP [dm6]	G	T	2.425e^-5	0.642	INTERGENIC
3R	12110222	3R_12110222_SNP [dm3] 3R_16284500_SNP [dm6]	T	C	2.432e^-5	0.642	INTRON gish	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	12109413	3R_12109413_SNP [dm3] 3R_16283691_SNP [dm6]	T	A	2.525e^-5	0.642	INTRON gish
3R	26301892	3R_26301892_SNP [dm3] 3R_30476170_SNP [dm6]	G	A	2.532e^-5	0.642	UPSTREAM spdo INTRON PH4alphaEFB	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	14081117	3L_14081117_SNP [dm3] 3L_14088017_SNP [dm6]	T	A	2.554e^-5	0.642	INTERGENIC
X	5388885	X_5388885_SNP [dm3] X_5494852_SNP [dm6]	T	C	2.590e^-5	0.642	NON_SYNONYMOUS_CODING frma DOWNSTREAM SPR
X	8916526	X_8916526_DEL [dm3] X_9022493_DEL [dm6]	ACAATCCCAA	A	2.617e^-5	0.642	INTRON CR43836 & 1 other
3R	12058421	3R_12058421_SNP [dm3] 3R_16232699_SNP [dm6]	G	A	2.619e^-5	0.642	INTRON tara	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	11551086	X_11551086_INS [dm3] X_11657053_INS [dm6]	C	CC	2.692e^-5	0.642	INTRON Ptp10D	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13202519	3R_13202519_SNP [dm3] 3R_17376797_SNP [dm6]	G	A	2.724e^-5	0.642	INTRON Brf
3L	12943182	3L_12943182_INS [dm3] 3L_12950082_INS [dm6]	T	TT	2.737e^-5	0.642	INTERGENIC
2L	6771736	2L_6771736_SNP [dm3] 2L_6771736_SNP [dm6]	A	C	2.740e^-5	0.642	UPSTREAM CG11321 INTRON CG11321
3L	5273681	3L_5273681_SNP [dm3] 3L_5280581_SNP [dm6]	G	C	3.002e^-5	0.691	INTERGENIC
X	13213291	X_13213291_SNP [dm3] X_13319258_SNP [dm6]	G	T	3.025e^-5	0.691	INTRON IP3K2
3L	20595178	3L_20595178_SNP [dm3] 3L_20602078_SNP [dm6]	G	A	3.062e^-5	0.691	INTRON knrl
2L	9413678	2L_9413678_SNP [dm3] 2L_9413678_SNP [dm6]	A	T	3.175e^-5	0.696	INTRON Shawl
2R	7891651	2R_7891651_SNP [dm3] 2R_12004146_SNP [dm6]	A	C	3.191e^-5	0.696	SYNONYMOUS_CODING otk
3L	2478087	3L_2478087_SNP [dm3] 3L_2478087_SNP [dm6]	T	G	3.240e^-5	0.696	INTRON CG45186 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12108896	3R_12108896_SNP [dm3] 3R_16283174_SNP [dm6]	A	G	3.240e^-5	0.696	INTRON gish	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1
3R	12105616	3R_12105616_SNP [dm3] 3R_16279894_SNP [dm6]	A	C	3.332e^-5	0.696	UPSTREAM gish INTRON gish	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Trl
3R	12109357	3R_12109357_SNP [dm3] 3R_16283635_SNP [dm6]	G	C	3.376e^-5	0.696	INTRON gish
3R	25296491	3R_25296491_SNP [dm3] 3R_29470769_SNP [dm6]	G	A	3.386e^-5	0.696	INTRON Ptp99A
3R	12106379	3R_12106379_DEL [dm3] 3R_16280657_DEL [dm6]	ATTAACGTA	A	3.394e^-5	0.696	UPSTREAM gish INTRON gish	TF binding site 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_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	4100363	X_4100363_SNP [dm3] X_4206330_SNP [dm6]	A	G	3.485e^-5	0.696	UPSTREAM Fas2 INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	4401147	3R_4401147_DEL [dm3] 3R_8575425_DEL [dm6]	TT	T	3.613e^-5	0.696	INTERGENIC
X	20453085	X_20453085_SNP [dm3] X_20582058_SNP [dm6]	G	T	3.643e^-5	0.696	INTERGENIC
2R	16998517	2R_16998517_SNP [dm3] 2R_21111012_SNP [dm6]	A	G	3.687e^-5	0.696	INTRON ktub
3L	10644477	3L_10644477_DEL [dm3] 3L_10651377_DEL [dm6]	CCC	A	3.706e^-5	0.696	INTRON CG32066
2L	5890117	2L_5890117_INS [dm3] 2L_5890117_INS [dm6]	A	AA	3.745e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
X	13213950	X_13213950_SNP [dm3] X_13319917_SNP [dm6]	C	T	3.771e^-5	0.696	INTRON IP3K2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	4388193	3R_4388193_SNP [dm3] 3R_8562471_SNP [dm6]	C	T	3.780e^-5	0.696	NON_SYNONYMOUS_CODING mRpS18A UPSTREAM CG31460 & 1 other DOWNSTREAM CR44291	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
3L	20595131	3L_20595131_SNP [dm3] 3L_20602031_SNP [dm6]	T	C	3.787e^-5	0.696	INTRON knrl

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

mn_Protein_Pooled phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results