JoGo: Joint Open Genome and Omics Platform

Haplotype Detail Info [BRCA2_chr13_32310508_32405268>a0005c0007t0026g0297]

geneid	675
ensemblid	ENSG00000139618.18
hgncid	1101
symbol	BRCA2
name	BRCA2 DNA repair associated
refseq_nuc	NM_000059.4
refseq_prot	NP_000050.3
ensembl_nuc	ENST00000380152.8
ensembl_prot	ENSP00000369497.3
mane_status	MANE Select
chr	chr13
start	32315508
end	32400268
strand	+
ver	v1.2
region	chr13:32315508-32400268
region5000	chr13:32310508-32405268
regionname0	BRCA2_chr13_32315508_32400268
regionname5000	BRCA2_chr13_32310508_32405268

chr:pos	ref	alt	af	annotation	impact	samples	AHAPIDS	ACHAPIDS	ACTHAPIDS	ACTGHAPIDS	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

chr:pos	ref	alt	af	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

chr:pos	ref	alt	af	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

chr:pos	ref	alt	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	af	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	ahapid	alen	total	AFR	AMR	EAS	EUR	SAS	aseq	chr	start	end
BRCA2	1/0	a0005	3418	9	7	1	0	0	0	subcellular location copy fasta	chr13	32310508	32405268

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	chapid	clen	total	AFR	AMR	EAS	EUR	SAS	cseq	chr	start	end
BRCA2	1/0	c0007	10257	7	5	1	0	0	0	copy fasta	chr13	32310508	32405268

genename	grch38/ chm13v2	thapid	tlen	total	AFR	AMR	EAS	EUR	SAS	tseq	chr	start	end
BRCA2	1/0	t0026	1698	1	0	0	0	0	0	copy fasta	chr13	32310508	32405268

genename	grch38/ chm13v2	ghapid	total	AFR	AMR	EAS	EUR	SAS	chr	start	end
BRCA2	1/0	g0297	1	0	0	0	0	0	chr13	32310508	32405268

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	achapid	total	AFR	AMR	EAS	EUR	SAS	clen	cseq	chr	start	end
BRCA2	1/0	a0005c0007	7	5	1	0	0	0	10257	copy fasta	chr13	32310508	32405268

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	acthapid	total	AFR	AMR	EAS	EUR	SAS	tlen	tseq	chr	start	end
BRCA2	1/0	a0005c0007t0026	1	0	0	0	0	0	11954	copy fasta	chr13	32310508	32405268

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	actghapid	total	AFR	AMR	EAS	EUR	SAS	chr	start	end
BRCA2	1/0	a0005c0007t0026g0297	1	0	0	0	0	0	chr13	32310508	32405268

pos	S. Strand	E# Exon Number	max	median	min	type	haplotypeid	max_hap_list	min_hap_list	symbol	chr	start	end
32315667	+	1	-0.5631	-0.5631	-0.5631	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32316422	+	2	0.9324	0.9324	0.9324	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32316527	+	2	-0.9121	-0.9121	-0.9121	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32319077	+	3	0.9711	0.9710	0.9711	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32319325	+	3	-0.9570	-0.9570	-0.9570	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32325076	+	4	0.9819	0.9819	0.9819	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32325184	+	4	-0.9933	-0.9933	-0.9933	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326101	+	5	0.9823	0.9823	0.9823	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326150	+	5	-0.9816	-0.9816	-0.9816	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326242	+	6	0.9794	0.9794	0.9794	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326282	+	6	-0.9804	-0.9804	-0.9804	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326499	+	7	0.7759	0.7759	0.7759	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32326613	+	7	-0.8182	-0.8182	-0.8182	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32329443	+	8	0.9952	0.9952	0.9952	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32329492	+	8	-0.9954	-0.9954	-0.9954	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32330919	+	9	0.9989	0.9989	0.9989	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32331030	+	9	-0.9987	-0.9987	-0.9987	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32332272	+	10	0.9950	0.9950	0.9950	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32333387	+	10	-0.9923	-0.9923	-0.9923	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32336265	+	11	0.9853	0.9853	0.9853	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32341196	+	11	-0.9537	-0.9537	-0.9537	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32344558	+	12	0.9792	0.9792	0.9792	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32344653	+	12	-0.9532	-0.9532	-0.9532	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32346827	+	13	0.9966	0.9966	0.9966	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32346896	+	13	-0.9974	-0.9974	-0.9974	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32354861	+	14	0.9684	0.9684	0.9684	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32355288	+	14	-0.9902	-0.9902	-0.9902	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32356428	+	15	0.9472	0.9472	0.9472	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32356609	+	15	-0.9783	-0.9783	-0.9783	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32357742	+	16	0.9945	0.9945	0.9945	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32357929	+	16	-0.9767	-0.9767	-0.9767	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32362523	+	17	0.9672	0.9672	0.9672	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32362693	+	17	-0.9280	-0.9280	-0.9280	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32363179	+	18	0.9838	0.9838	0.9838	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32363533	+	18	-0.9343	-0.9343	-0.9343	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32370402	+	19	0.9882	0.9882	0.9882	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32370557	+	19	-0.9607	-0.9607	-0.9607	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32370956	+	20	0.9213	0.9213	0.9213	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32371100	+	20	-0.9857	-0.9857	-0.9857	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32376670	+	21	0.9973	0.9972	0.9973	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32376791	+	21	-0.9931	-0.9931	-0.9931	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32379317	+	22	0.9898	0.9898	0.9898	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32379515	+	22	-0.9890	-0.9890	-0.9890	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32379750	+	23	0.8997	0.8997	0.8997	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32379913	+	23	-0.9329	-0.9329	-0.9329	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32380007	+	24	0.9955	0.9955	0.9955	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32380145	+	24	-0.9985	-0.9985	-0.9985	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32394689	+	25	0.9970	0.9970	0.9970	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32394933	+	25	-0.9980	-0.9980	-0.9980	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32396898	+	26	0.9952	0.9952	0.9952	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32397044	+	26	-0.9971	-0.9971	-0.9971	acceptor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268
32398162	+	27	0.9584	0.9584	0.9584	donor	a0005c0007t0026g0297	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	homoSapiens_grch38.hp1 homoSapiens_grch38.hp1	BRCA2	chr13	32310508	32405268

pos	annotation hgvs_c hgvs_p	clinvarid	clnsig	geneinfo	mc	clndisdb	strand strand	ahapid ahapid_count	chapid chapid count	thapid thapid_count	ghapid ghapid_count	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	impact	chr	ref	alt	external

CHR:POS	annotation hgvs_c hgvs_p	disease trait -log10p odds or beta	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	study	initial sample size/ replication sample size	report genes	mapped gene	strongest snp risk allele	strand strand	impact	chr	ref	alt

pos	genename hgvs_c hgvs_p annotation	tissue expression gene -log10(pval) slope Tissue name in GTEx database(the target eQTL tissue name of the GTEx database) The -log10(nominal pvalue) in GTEx database Slope in GTEx database (positive value:alt allele has higher gene expression)	ahapid chapid thapid ghapid ahapid_count chapid_count thapid_count ghapid_count	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	af allele frequency in GTEx database	ms The number of samples with minor allele in GTEx database	ma The number of minor allele count in GTEx database	ver GTEx version	vid Variant ID in GTEx database	strand strand	impact	chr	ref	alt	external

Haplotype Detail Info [BRCA2_chr13_32310508_32405268>a0005c0007t0026g0297]

🧬 Gene Summary

🧬 JoGo Online Haplotype Explorer BRCA2_chr13_32310508_32405268

AVariants in Amino-acids (protein) level Haplotype (Total: 0)

CVariants in Coding level Haplotype (Total: 0)

TVariants in Transcript level Haplotype (Total: 0)

GVariants in Genebody level Haplotype (Total: 0)

AAmino-acid (protein) Level Haplotype Info (Total: 1)

CCoding Level Haplotype Info (Total: 1)

TTranscript Level Haplotype Info (Total: 1)

GGenebody Level Haplotype Info (Total: 1)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 1)

A C T ACT Level (Amino Acid + Coding + Transcript) Haplotype Info (Total: 1)

A C T G ACTG Level (Amino Acid + Coding + Transcript + Genebody) Haplotype Info (Total: 1)

📊 HaplotypeQTL Info

⚡ Splicing Related Variants (Total: 52)

🩺 Clinvar Related Variants (Total: 0)

GWASCatalog Related Variants (Total: 0)

GTEx Related Variants (Page 1 of 1 - Total: 0)