JoGo: Joint Open Genome and Omics Platform

Search by Genic region

geneid	203611
ensemblid	ENSG00000129873.8
hgncid	23921
symbol	CDY2B
name	chromodomain Y-linked 2B
refseq_nuc	NM_001001722.2
refseq_prot	NP_001001722.1
ensembl_nuc	ENST00000382867.4
ensembl_prot	ENSP00000372319.3
mane_status	MANE Select
chr	chrY
start	17878260
end	17880220
strand	-
ver	v1.2
region	chrY:17878260-17880220
region5000	chrY:17873260-17885220
regionname0	CDY2B_chrY_17878260_17880220
regionname5000	CDY2B_chrY_17873260_17885220

ahapid	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	alen	total	AFR	AMR	EAS	EUR	SAS	JPT	regionname	genename	aa	chr	start	end
a0001	0/0	541	52	5	18	12	3	14	9	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
a0002	0/0	541	1	0	0	0	0	1	0	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220

chapid	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	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
c0001	0/0	1626	52	5	18	12	3	14	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
c0002	0/0	1626	1	0	0	0	0	1	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220

thapid	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	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
t0001	0/0	336	37	5	11	12	1	8	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
t0002	0/0	336	16	0	7	0	2	7	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220

ghapid	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	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
g0000	0/0	53	5	18	12	3	15	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220

achapid	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	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
a0001c0001	0/0	1626	52	5	18	12	3	14	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
a0002c0002	0/0	1626	1	0	0	0	0	1	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1961	36	5	11	12	1	7	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
a0001c0001t0002	0/0	1961	16	0	7	0	2	7	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220
a0002c0002t0001	0/0	1961	1	0	0	0	0	1	CDY2B_chrY_17873260_17885220	CDY2B	copy fasta	chrY	17873260	17885220

actghapid	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	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
a0001c0001t0001g0000	0/0	36	5	11	12	1	7	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
a0001c0001t0002g0000	0/0	16	0	7	0	2	7	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
a0002c0002t0001g0000	0/0	1	0	0	0	0	1	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00642	hp1	a0001	c0001	t0002	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG00738	hp1	a0001	c0001	t0002	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01074	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01099	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01106	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01109	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01167	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01243	hp1	a0001	c0001	t0002	g0000	AMR	PUR	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01255	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01256	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01258	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01261	hp1	a0001	c0001	t0002	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01358	hp1	a0001	c0001	t0002	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01433	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01515	hp1	a0001	c0001	t0002	g0000	EUR	IBS	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01928	hp1	a0001	c0001	t0001	g0000	AMR	PEL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01934	hp1	a0001	c0001	t0002	g0000	AMR	PEL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01943	hp1	a0001	c0001	t0002	g0000	AMR	PEL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG01952	hp1	a0001	c0001	t0001	g0000	AMR	PEL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02040	hp1	a0001	c0001	t0001	g0000	EAS	KHV	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02132	hp1	a0001	c0001	t0001	g0000	EAS	KHV	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02602	hp1	a0001	c0001	t0002	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02698	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02717	hp1	a0001	c0001	t0001	g0000	AFR	GWD	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02735	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG02738	hp1	a0001	c0001	t0002	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03017	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03098	hp1	a0001	c0001	t0001	g0000	AFR	MSL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03130	hp1	a0001	c0001	t0001	g0000	AFR	ESN	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03490	hp1	a0001	c0001	t0002	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03492	hp1	a0001	c0001	t0002	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03579	hp1	a0001	c0001	t0001	g0000	AFR	MSL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03654	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03688	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG03710	hp1	a0002	c0002	t0001	g0000	SAS	PJL	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG04115	hp1	a0001	c0001	t0002	g0000	SAS	STU	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG04199	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG04204	hp1	a0001	c0001	t0002	g0000	SAS	STU	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
HG04228	hp1	a0001	c0001	t0002	g0000	SAS	STU	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18522	hp1	a0001	c0001	t0001	g0000	AFR	YRI	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18612	hp1	a0001	c0001	t0001	g0000	EAS	CHB	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18940	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18974	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18983	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA18995	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA19006	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA19056	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA19068	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA19079	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA19091	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA20752	hp2	a0001	c0001	t0002	g0000	EUR	TSI	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA20805	hp1	a0001	c0001	t0001	g0000	EUR	TSI	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220
NA20905	hp1	a0001	c0001	t0001	g0000	SAS	GIH	CDY2B_chrY_17873260_17885220	CDY2B	chrY	17873260	17885220

chr:pos	ref	alt	# # of ahapid:amino-acid(protein) level	ahapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:17878397	C C	T T	1	a0002 a0002	1	HG03710.hp1 HG03710.hp1	missense_variant	MODERATE	c.1496G>A c.1496G>A	p.Arg499His p.Arg499His	CDY2B	ENSG00000129873.8	transcript	ENST00000382867.4	protein_coding	1/1	1824/1961	1496/1626	499/541			chrY	17878397

chr:pos	ref	alt	# # of chapid	chapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos

chr:pos	ref	alt	# # of thapid:transcript level	thapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:17880120	G G	A A	2	a0001c0001t0001 a0002c0002t0001 a0001c0001t0001 a0002c0002t0001	37	HG01074.hp1 HG01099.hp1 HG01106.hp1 others(34): Show HG01074.hp1 HG01099.hp1 HG01106.hp1 HG01109.hp1 HG01167.hp1 HG01255.hp1 HG01256.hp1 HG01258.hp1 HG01433.hp1 HG01928.hp1 HG01952.hp1 HG02040.hp1 HG02132.hp1 HG02698.hp1 HG02717.hp1 HG02735.hp1 HG03017.hp1 HG03098.hp1 HG03130.hp1 HG03579.hp1 HG03654.hp1 HG03688.hp1 HG03710.hp1 HG04199.hp1 NA18522.hp1 NA18612.hp1 NA18940.hp1 NA18974.hp1 NA18983.hp1 NA18995.hp1 NA19006.hp1 NA19056.hp1 NA19068.hp1 NA19079.hp1 NA19091.hp1 NA20805.hp1 NA20905.hp1	5_prime_UTR_premature_start_codon_gain_variant	LOW	c.-228C>T c.-228C>T		CDY2B	ENSG00000129873.8	transcript	ENST00000382867.4	protein_coding	1/1						chrY	17880120

chr:pos	ref	alt	# # of ghapid:genebody level	ghapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	genebody_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos

Search by Genic region

Search

🧬 JoGo Online Haplotype Explorer CDY2B_chrY_17873260_17885220

JoGo Local Haplotype Explorer (on iGV) CDY2B_chrY_17873260_17885220

Translation Multiple Alignment View

ACTG-Haplotype Mutation Positions 3D Viewer

🧬 Gene Summary

AAmino acid(protein) Level Haplotype Info (Total: 2)

CCoding Level Haplotype Info (Total: 2)

TTranscript Level Haplotype Info (Total: 2)

GGenebody Level Haplotype Info (Total: 1)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 2)

A C T ACT Level (Amino Acid + Coding + Transcript) Haplotype Info (Total: 3)

A C T G ACTG Level (Amino Acid + Coding + Transcript + Genebody) Haplotype Info (Total: 3)

Haplotype Details by Sample (Haploid Level) (Total: 53)

AAmino acid(protein) Level Haplotype Related Variants (Effect to Protein Coding Variants) (Total: 1)

CCoding Level Variants (Synonymous Mutations) (Total: 0)

TTranscript Level Haplotype Variants (5'UTR+3'UTR) (Total: 1)

GGenebody Level Haplotype Variants (Intron) (Total: 0)

External Link

Annotation (Repeats)

Annotation (SNP Array)