JoGo: Joint Open Genome and Omics Platform

Haplotype Detail Info [AAMP_chr2_218259129_218275137>a0001c0001t0002g0045]

geneid	14
ensemblid	ENSG00000127837.10
hgncid	18
symbol	AAMP
name	angio associated migratory cell protein
refseq_nuc	NM_001087.5
refseq_prot	NP_001078.2
ensembl_nuc	ENST00000248450.9
ensembl_prot	ENSP00000248450.4
mane_status	MANE Select
chr	chr2
start	218264129
end	218270137
strand	-
ver	v1.2
region	chr2:218264129-218270137
region5000	chr2:218259129-218275137
regionname0	AAMP_chr2_218264129_218270137
regionname5000	AAMP_chr2_218259129_218275137

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
chr2:218267925	T T	A A	intron_variant intron_variant	MODIFIER	HG02922.hp1 HG02922.hp1	a0001 a0001	a0001c0001 a0001c0001	a0001c0001t0002 a0001c0001t0002	a0001c0001t0002g0045 a0001c0001t0002g0045	1	400	0.0025	0	AAMP	ENSG00000127837.10	transcript	ENST00000248450.9	protein_coding	2/10	c.275-312A>T

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
AAMP	1/1	a0001	434	376	92	75	154	16	37	subcellular location copy fasta	chr2	218259129	218275137

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
AAMP	1/1	c0001	1305	369	89	75	152	16	35	copy fasta	chr2	218259129	218275137

genename	grch38/ chm13v2	thapid	tlen	total	AFR	AMR	EAS	EUR	SAS	tseq	chr	start	end
AAMP	1/0	t0002	456	18	17	0	0	0	0	copy fasta	chr2	218259129	218275137

genename	grch38/ chm13v2	ghapid	total	AFR	AMR	EAS	EUR	SAS	chr	start	end
AAMP	0/0	g0045	1	1	0	0	0	0	chr2	218259129	218275137

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
AAMP	1/1	a0001c0001	369	89	75	152	16	35	1305	copy fasta	chr2	218259129	218275137

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
AAMP	1/0	a0001c0001t0002	18	17	0	0	0	0	1760	copy fasta	chr2	218259129	218275137

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
AAMP	0/0	a0001c0001t0002g0045	1	1	0	0	0	0	chr2	218259129	218275137

pos	S. Strand	E# Exon Number	max	median	min	type	haplotypeid	max_hap_list	min_hap_list	symbol	chr	start	end
218269966	-	1	-0.9847	-0.9847	-0.9847	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218269382	-	2	-0.9955	-0.9955	-0.9955	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218269534	-	2	0.9635	0.9635	0.9635	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218267494	-	3	-0.9978	-0.9978	-0.9978	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218267613	-	3	0.9856	0.9856	0.9856	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266847	-	4	-0.9975	-0.9975	-0.9975	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266986	-	4	0.9827	0.9827	0.9827	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266443	-	5	-0.9656	-0.9656	-0.9656	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266587	-	5	0.9677	0.9677	0.9677	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266064	-	6	-0.9740	-0.9740	-0.9740	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218266147	-	6	0.9741	0.9741	0.9741	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265831	-	7	-0.9983	-0.9983	-0.9983	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265946	-	7	0.9853	0.9853	0.9853	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265579	-	8	-0.9438	-0.9438	-0.9438	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265682	-	8	0.9477	0.9476	0.9477	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265371	-	9	-0.9847	-0.9847	-0.9847	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265461	-	9	0.9729	0.9729	0.9729	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265020	-	10	-0.9984	-0.9984	-0.9984	acceptor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218265174	-	10	0.9922	0.9922	0.9922	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137
218264608	-	11	0.7564	0.7564	0.7564	donor	a0001c0001t0002g0045	HG02922.hp1 HG02922.hp1	HG02922.hp1 HG02922.hp1	AAMP	chr2	218259129	218275137

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
218270431:splice 218270431:variant goto	c.-345T>A c.-345T>A	334304	Likely_benign	PNKD:25953 LOC129935594:129935594 PNKD:25953 LOC129935594:129935594	. .	MONDO:MONDO:0700089 MedGen:C4551506 OMIM:118800 Orphanet:98810\|MedGen:C3661900 MONDO:MONDO:0700089 MedGen:C4551506 OMIM:118800 Orphanet:98810\|MedGen:C3661900	-	1	1	1	3	a0001 a0001	a0001c0001 a0001c0001	a0001c0001t0002 a0001c0001t0002	a0001c0001t0002g0007 a0001c0001t0002g0045 a0001c0001t0002g0051 a0001c0001t0002g0007 a0001c0001t0002g0045 a0001c0001t0002g0051	HG01884.hp1 HG02572.hp2 HG02897.hp1 HG02922.hp1 HG03130.hp2 others(1): Show HG01884.hp1 HG02572.hp2 HG02897.hp1 HG02922.hp1 HG03130.hp2 HG03540.hp1	MODIFIER	chr2	A A	T T	TogoVar

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 [AAMP_chr2_218259129_218275137>a0001c0001t0002g0045]

🧬 Gene Summary

🧬 JoGo Online Haplotype Explorer AAMP_chr2_218259129_218275137

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: 1)

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: 20)

🩺 Clinvar Related Variants (Total: 1)

GWASCatalog Related Variants (Total: 0)

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