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=4.747e^-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

Covariate	p-value	Significance
In_3R_K	0.06716

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.8898	0.0867

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1894 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	10836895	3L_10836895_SNP [dm3] 3L_10843795_SNP [dm6]	A	G	7.532e^-7	0.66	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2R	9676496	2R_9676496_SNP [dm3] 2R_13788991_SNP [dm6]	T	C	7.843e^-7	0.66	INTERGENIC
2R	5389944	2R_5389944_SNP [dm3] 2R_9502439_SNP [dm6]	C	A	1.064e^-6	0.66	NON_SYNONYMOUS_CODING Wnt2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	1354357	2R_1354357_SNP [dm3] 2R_5466852_SNP [dm6]	G	T	2.034e^-6	0.66	INTERGENIC	transposable element FlyBase
2R	14676098	2R_14676098_SNP [dm3] 2R_18788593_SNP [dm6]	C	T	2.884e^-6	0.66	INTRON CG15080
2R	9799311	2R_9799311_SNP [dm3] 2R_13911806_SNP [dm6]	C	T	3.443e^-6	0.66	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	16925265	X_16925265_SNP [dm3] X_17031232_SNP [dm6]	G	C	3.486e^-6	0.66	INTRON CG45002
2R	9799329	2R_9799329_INS [dm3] 2R_13911824_INS [dm6]	A	TGATGGTG	3.520e^-6	0.66	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799332	2R_9799332_SNP [dm3] 2R_13911827_SNP [dm6]	A	G	3.520e^-6	0.66	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799335	2R_9799335_SNP [dm3] 2R_13911830_SNP [dm6]	C	T	3.520e^-6	0.66	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9675820	2R_9675820_SNP [dm3] 2R_13788315_SNP [dm6]	T	A	4.789e^-6	0.771	DOWNSTREAM Cpr50Ca INTERGENIC
2R	12145282	2R_12145282_SNP [dm3] 2R_16257777_SNP [dm6]	C	A	4.931e^-6	0.771	INTRON CngA
3L	10836651	3L_10836651_SNP [dm3] 3L_10843551_SNP [dm6]	C	T	5.545e^-6	0.792	INTERGENIC	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9676653	2R_9676653_SNP [dm3] 2R_13789148_SNP [dm6]	G	A	6.104e^-6	0.792	INTERGENIC
X	16925264	X_16925264_SNP [dm3] X_17031231_SNP [dm6]	G	A	6.336e^-6	0.792	INTRON CG45002
2R	9679611	2R_9679611_DEL [dm3] 2R_13792106_DEL [dm6]	CC	C	7.854e^-6	0.812	EXON CR43811
3L	12494166	3L_12494166_SNP [dm3] 3L_12501066_SNP [dm6]	C	T	8.045e^-6	0.812	UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
2L	20423664	2L_20423664_SNP [dm3] 2L_20423664_SNP [dm6]	G	A	8.059e^-6	0.812	DOWNSTREAM Arpc2 INTRON CG15130
2R	1354359	2R_1354359_SNP [dm3] 2R_5466854_SNP [dm6]	C	A	8.268e^-6	0.812	INTERGENIC	transposable element FlyBase
2R	17647628	2R_17647628_SNP [dm3] 2R_21760123_SNP [dm6]	C	A	8.662e^-6	0.812	INTERGENIC
2R	12145295	2R_12145295_DEL [dm3] 2R_16257790_DEL [dm6]	ATTGA	A	1.202e^-5	0.926	INTRON CngA
2R	7220740	2R_7220740_SNP [dm3] 2R_11333235_SNP [dm6]	C	T	1.245e^-5	0.926	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	13384648	2R_13384648_SNP [dm3] 2R_17497143_SNP [dm6]	G	A	1.282e^-5	0.926	INTERGENIC
X	5014255	X_5014255_DEL [dm3] X_5120222_DEL [dm6]	ACCA	A	1.369e^-5	0.926	INTRON rg & 1 other
3R	16300782	3R_16300782_SNP [dm3] 3R_20475060_SNP [dm6]	T	C	1.387e^-5	0.926	INTRON Gfrl
3R	19207896	3R_19207896_SNP [dm3] 3R_23382174_SNP [dm6]	T	A	1.437e^-5	0.926	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	1352419	2R_1352419_SNP [dm3] 2R_5464914_SNP [dm6]	G	T	1.464e^-5	0.926	INTERGENIC	transposable element FlyBase
2R	8620603	2R_8620603_SNP [dm3] 2R_12733098_SNP [dm6]	T	C	1.475e^-5	0.926	INTRON CG42663	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	20191493	2R_20191493_SNP [dm3] 2R_24303970_SNP [dm6]	G	A	1.622e^-5	0.926	INTERGENIC	regulatory region REDfly_CRMs
2L	19688097	2L_19688097_SNP [dm3] 2L_19688097_SNP [dm6]	T	A	1.688e^-5	0.926	INTRON Lar	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA transposable element FlyBase
2L	10430998	2L_10430998_SNP [dm3] 2L_10430998_SNP [dm6]	T	A	1.710e^-5	0.926	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	8151847	3R_8151847_SNP [dm3] 3R_12326125_SNP [dm6]	C	T	1.725e^-5	0.926	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	12145306	2R_12145306_SNP [dm3] 2R_16257801_SNP [dm6]	A	G	1.812e^-5	0.926	INTRON CngA
2L	8423456	2L_8423456_DEL [dm3] 2L_8423456_DEL [dm6]	TGCT	T	1.846e^-5	0.926	INTRON Akap200	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
3L	10836872	3L_10836872_SNP [dm3] 3L_10843772_SNP [dm6]	G	T	1.905e^-5	0.926	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2R	17647629	2R_17647629_SNP [dm3] 2R_21760124_SNP [dm6]	T	A	1.938e^-5	0.926	INTERGENIC
2R	14925367	2R_14925367_SNP [dm3] 2R_19037862_SNP [dm6]	A	G	1.944e^-5	0.926	INTERGENIC
2R	7220722	2R_7220722_SNP [dm3] 2R_11333217_SNP [dm6]	G	A	1.949e^-5	0.926	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	20517634	3R_20517634_SNP [dm3] 3R_24691912_SNP [dm6]	C	T	1.987e^-5	0.926	SYNONYMOUS_CODING slo
2R	7220794	2R_7220794_SNP [dm3] 2R_11333289_SNP [dm6]	T	C	1.989e^-5	0.926	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	10431178	2L_10431178_SNP [dm3] 2L_10431178_SNP [dm6]	A	T	2.049e^-5	0.926	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	8151852	3R_8151852_SNP [dm3] 3R_12326130_SNP [dm6]	C	G	2.073e^-5	0.926	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
X	6732826	X_6732826_SNP [dm3] X_6838793_SNP [dm6]	T	A	2.125e^-5	0.927	UTR_3_PRIME CG14435 DOWNSTREAM nonC & 1 other
3L	12494061	3L_12494061_SNP [dm3] 3L_12500961_SNP [dm6]	T	C	2.339e^-5	0.947	NON_SYNONYMOUS_CODING CG10638 UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
2L	18814298	2L_18814298_SNP [dm3] 2L_18814298_SNP [dm6]	T	C	2.366e^-5	0.947	DOWNSTREAM CG17325 & 1 other INTERGENIC
2R	12073056	2R_12073056_SNP [dm3] 2R_16185551_SNP [dm6]	A	G	2.414e^-5	0.947	SYNONYMOUS_CODING CG8441 DOWNSTREAM Lis-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	17647635	2R_17647635_INS [dm3] 2R_21760130_INS [dm6]	C	CC	2.434e^-5	0.947	INTERGENIC
2R	9675391	2R_9675391_SNP [dm3] 2R_13787886_SNP [dm6]	G	A	2.448e^-5	0.947	DOWNSTREAM Cpr50Ca INTERGENIC
2R	9798932	2R_9798932_SNP [dm3] 2R_13911427_SNP [dm6]	G	A	2.474e^-5	0.947	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10368541	3R_10368541_SNP [dm3] 3R_14542819_SNP [dm6]	G	C	2.596e^-5	0.974	INTRON Pde6
2R	12074021	2R_12074021_SNP [dm3] 2R_16186516_SNP [dm6]	C	A	2.741e^-5	0.978	UPSTREAM clu & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Ubx
X	4799123	X_4799123_SNP [dm3] X_4905090_SNP [dm6]	A	T	2.931e^-5	0.978	SYNONYMOUS_CODING CG42594 UTR_3_PRIME CG42594	TF binding site mE1_TFBS_chinmo
3R	13660339	3R_13660339_SNP [dm3] 3R_17834617_SNP [dm6]	A	G	2.977e^-5	0.978	INTRON tinc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	14925188	2R_14925188_SNP [dm3] 2R_19037683_SNP [dm6]	A	G	3.009e^-5	0.978	INTERGENIC
2L	18814299	2L_18814299_SNP [dm3] 2L_18814299_SNP [dm6]	A	G	3.043e^-5	0.978	DOWNSTREAM CG17325 & 1 other INTERGENIC
2L	22569694	2L_22569694_SNP [dm3] 2L_22676962_SNP [dm6]	A	G	3.151e^-5	0.978	INTRON CG40006
2L	10431186	2L_10431186_SNP [dm3] 2L_10431186_SNP [dm6]	A	G	3.155e^-5	0.978	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	19573478	2R_19573478_SNP [dm3] 2R_23685955_SNP [dm6]	C	T	3.193e^-5	0.978	UPSTREAM l_2_efl INTRON St3
3R	8151848	3R_8151848_SNP [dm3] 3R_12326126_SNP [dm6]	T	G	3.358e^-5	0.978	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	12100255	2R_12100255_SNP [dm3] 2R_16212750_SNP [dm6]	T	C	3.379e^-5	0.978	INTRON mrj
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	3.494e^-5	0.978	INTRON Spn
2R	12076005	2R_12076005_SNP [dm3] 2R_16188500_SNP [dm6]	C	T	3.574e^-5	0.978	INTRON clu	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	17002143	2R_17002143_SNP [dm3] 2R_21114638_SNP [dm6]	A	C	3.691e^-5	0.978	INTRON ktub
X	9006441	X_9006441_INS [dm3] X_9112408_INS [dm6]	C	CTT	3.718e^-5	0.978	INTRON AP-1gamma
X	16925193	X_16925193_SNP [dm3] X_17031160_SNP [dm6]	A	T	3.838e^-5	0.978	INTRON CG45002
3L	5212948	3L_5212948_SNP [dm3] 3L_5219848_SNP [dm6]	T	C	3.839e^-5	0.978	INTRON shep
3L	2545690	3L_2545690_SNP [dm3] 3L_2545690_SNP [dm6]	G	A	3.877e^-5	0.978	INTRON Spn
2R	9675734	2R_9675734_SNP [dm3] 2R_13788229_SNP [dm6]	T	C	3.922e^-5	0.978	DOWNSTREAM Cpr50Ca INTERGENIC
2R	15540432	2R_15540432_SNP [dm3] 2R_19652927_SNP [dm6]	C	T	3.954e^-5	0.978	UPSTREAM CR44213 DOWNSTREAM Ir56e EXON CR44212
3L	10767055	3L_10767055_SNP [dm3] 3L_10773955_SNP [dm6]	A	G	3.974e^-5	0.978	DOWNSTREAM CG43245 INTERGENIC
X	8100507	X_8100507_SNP [dm3] X_8206474_SNP [dm6]	C	A	4.087e^-5	0.978	INTRON sdt
2R	8114508	2R_8114508_SNP [dm3] 2R_12227003_SNP [dm6]	C	T	4.103e^-5	0.978	UPSTREAM CG8854 INTRON CG8854
2R	7220854	2R_7220854_SNP [dm3] 2R_11333349_SNP [dm6]	T	C	4.194e^-5	0.978	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	16925175	X_16925175_SNP [dm3] X_17031142_SNP [dm6]	A	G	4.243e^-5	0.978	INTRON CG45002
2R	10033109	2R_10033109_SNP [dm3] 2R_14145604_SNP [dm6]	C	T	4.465e^-5	0.978	UPSTREAM mir-989 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
X	15295921	X_15295921_DEL [dm3] X_15401888_DEL [dm6]	AA	A	4.467e^-5	0.978	INTRON Cngl
3R	1742137	3R_1742137_SNP [dm3] 3R_5916415_SNP [dm6]	A	G	4.474e^-5	0.978	INTRON CG34113
2L	5718115	2L_5718115_SNP [dm3] 2L_5718115_SNP [dm6]	A	C	4.579e^-5	0.978	DOWNSTREAM CG11149 & 1 other INTERGENIC
2R	9677964	2R_9677964_SNP [dm3] 2R_13790459_SNP [dm6]	A	T	4.657e^-5	0.978	INTERGENIC
2R	14456857	2R_14456857_SNP [dm3] 2R_18569352_SNP [dm6]	T	A	4.797e^-5	0.978	INTRON GEFmeso	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	5014243	X_5014243_SNP [dm3] X_5120210_SNP [dm6]	G	C	4.857e^-5	0.978	INTRON rg & 1 other
2R	14925361	2R_14925361_INS [dm3] 2R_19037856_INS [dm6]	A	AA	4.954e^-5	0.978	INTERGENIC
2R	9675960	2R_9675960_SNP [dm3] 2R_13788455_SNP [dm6]	G	A	5.006e^-5	0.978	DOWNSTREAM Cpr50Ca INTERGENIC
2R	10011581	2R_10011581_SNP [dm3] 2R_14124076_SNP [dm6]	C	T	5.033e^-5	0.978	INTRON Prosap
2R	16443782	2R_16443782_SNP [dm3] 2R_20556277_SNP [dm6]	C	T	5.070e^-5	0.978	UPSTREAM lms INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	11943626	2R_11943626_SNP [dm3] 2R_16056121_SNP [dm6]	G	C	5.121e^-5	0.978	INTRON CG8405
X	16947237	X_16947237_SNP [dm3] X_17053204_SNP [dm6]	C	G	5.210e^-5	0.978	INTRON CG45002
2R	17929699	2R_17929699_SNP [dm3] 2R_22042194_SNP [dm6]	A	G	5.234e^-5	0.978	SYNONYMOUS_CODING PpD5	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	9702820	3R_9702820_SNP [dm3] 3R_13877098_SNP [dm6]	C	T	5.272e^-5	0.978	UTR_5_PRIME E5	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	7900843	2R_7900843_SNP [dm3] 2R_12013338_SNP [dm6]	G	A	5.279e^-5	0.978	INTRON otk	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2R	9977790	2R_9977790_SNP [dm3] 2R_14090285_SNP [dm6]	T	A	5.328e^-5	0.978	UPSTREAM CG42287 & 1 other INTRON Prosap
2R	9679289	2R_9679289_SNP [dm3] 2R_13791784_SNP [dm6]	T	G	5.403e^-5	0.978	UPSTREAM CR43811 INTERGENIC
2R	10011586	2R_10011586_SNP [dm3] 2R_14124081_SNP [dm6]	A	T	5.447e^-5	0.978	INTRON Prosap
2R	11943683	2R_11943683_SNP [dm3] 2R_16056178_SNP [dm6]	C	T	5.576e^-5	0.978	INTRON CG8405
3L	18957937	3L_18957937_SNP [dm3] 3L_18964837_SNP [dm6]	A	C	5.618e^-5	0.978	INTERGENIC
3L	18957938	3L_18957938_SNP [dm3] 3L_18964838_SNP [dm6]	T	A	5.618e^-5	0.978	INTERGENIC
X	9006430	X_9006430_SNP [dm3] X_9112397_SNP [dm6]	G	A	5.690e^-5	0.978	INTRON AP-1gamma
X	16947242	X_16947242_SNP [dm3] X_17053209_SNP [dm6]	A	G	5.698e^-5	0.978	INTRON CG45002
2L	15140673	2L_15140673_SNP [dm3] 2L_15140673_SNP [dm6]	C	T	5.824e^-5	0.978	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	5216153	3L_5216153_SNP [dm3] 3L_5223053_SNP [dm6]	T	A	5.909e^-5	0.978	INTRON shep

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

mn_Week1_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results