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geneid	9426
ensemblid	ENSG00000182415.11
hgncid	1810
symbol	CDY2A
name	chromodomain Y-linked 2A
refseq_nuc	NM_004825.2
refseq_prot	NP_004816.1
ensembl_nuc	ENST00000250838.6
ensembl_prot	ENSP00000250838.4
mane_status	MANE Select
chr	chrY
start	18025787
end	18027746
strand	+
ver	v1.2
region	chrY:18025787-18027746
region5000	chrY:18020787-18032746
regionname0	CDY2A_chrY_18025787_18027746
regionname5000	CDY2A_chrY_18020787_18032746

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	63	9	15	22	3	14	22	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0002	0/0	541	2	0	1	0	1	0	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0003	0/0	541	1	0	0	0	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0004	0/0	541	1	0	1	0	0	0	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746

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	63	9	15	22	3	14	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
c0002	0/0	1626	2	0	1	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
c0003	0/0	1626	1	0	1	0	0	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
c0004	0/0	1626	1	0	0	0	0	1	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746

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	335	66	9	17	22	3	15	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
t0002	0/0	335	1	0	0	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746

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	67	9	17	22	4	15	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746

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	63	9	15	22	3	14	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0002c0002	0/0	1626	2	0	1	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0003c0004	0/0	1626	1	0	0	0	0	1	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0004c0003	0/0	1626	1	0	1	0	0	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1960	62	9	15	22	2	14	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0001c0001t0002	0/0	1960	1	0	0	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0002c0002t0001	0/0	1960	2	0	1	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0003c0004t0001	0/0	1960	1	0	0	0	0	1	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746
a0004c0003t0001	0/0	1960	1	0	1	0	0	0	CDY2A_chrY_18020787_18032746	CDY2A	copy fasta	chrY	18020787	18032746

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	62	9	15	22	2	14	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
a0001c0001t0002g0000	0/0	1	0	0	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
a0002c0002t0001g0000	0/0	2	0	1	0	1	0	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
a0003c0004t0001g0000	0/0	1	0	0	0	0	1	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
a0004c0003t0001g0000	0/0	1	0	1	0	0	0	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00140	hp1	a0002	c0002	t0001	g0000	EUR	GBR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG00642	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG00738	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01069	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01074	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01099	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01109	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01167	hp2	a0002	c0002	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01192	hp1	a0004	c0003	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01243	hp1	a0001	c0001	t0001	g0000	AMR	PUR	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01255	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01256	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01258	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01261	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01358	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01433	hp1	a0001	c0001	t0001	g0000	AMR	CLM	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01515	hp1	a0001	c0001	t0001	g0000	EUR	IBS	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01934	hp1	a0001	c0001	t0001	g0000	AMR	PEL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG01943	hp1	a0001	c0001	t0001	g0000	AMR	PEL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02145	hp1	a0001	c0001	t0001	g0000	AFR	ACB	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02602	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02698	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02717	hp1	a0001	c0001	t0001	g0000	AFR	GWD	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02735	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02738	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02895	hp1	a0001	c0001	t0001	g0000	AFR	GWD	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02965	hp1	a0001	c0001	t0001	g0000	AFR	ESN	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03017	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03139	hp1	a0001	c0001	t0001	g0000	AFR	ESN	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03209	hp1	a0001	c0001	t0001	g0000	AFR	MSL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03490	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03492	hp1	a0001	c0001	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03579	hp1	a0001	c0001	t0001	g0000	AFR	MSL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03654	hp1	a0003	c0004	t0001	g0000	SAS	PJL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03688	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03942	hp1	a0001	c0001	t0001	g0000	SAS	BEB	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG04115	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG04199	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG04204	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG04228	hp1	a0001	c0001	t0001	g0000	SAS	STU	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18940	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18959	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18961	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18962	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18965	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18971	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18974	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18985	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18988	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18989	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18995	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19006	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19007	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19056	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19068	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19075	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19079	hp2	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19082	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19083	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19089	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA19091	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA20752	hp1	a0001	c0001	t0002	g0000	EUR	TSI	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA20805	hp1	a0001	c0001	t0001	g0000	EUR	TSI	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA20905	hp1	a0001	c0001	t0001	g0000	SAS	GIH	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG02486	hp1	a0001	c0001	t0001	g0000	AFR	ACB	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
HG03471	hp1	a0001	c0001	t0001	g0000	AFR	MSL	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746
NA18955	hp1	a0001	c0001	t0001	g0000	EAS	JPT	CDY2A_chrY_18020787_18032746	CDY2A	chrY	18020787	18032746

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	chr	pos
chrY:18026284	G G	A A	1	a0002 a0002	2	HG00140.hp1 HG01167.hp2 HG00140.hp1 HG01167.hp2	missense_variant	MODERATE	c.170G>A c.170G>A	p.Arg57Gln p.Arg57Gln	CDY2A	ENSG00000182415.11	transcript	ENST00000250838.6	protein_coding	1/1	498/1960	170/1626	57/541	chrY	18026284
chrY:18026556	T T	C C	1	a0004 a0004	1	HG01192.hp1 HG01192.hp1	missense_variant	MODERATE	c.442T>C c.442T>C	p.Phe148Leu p.Phe148Leu	CDY2A	ENSG00000182415.11	transcript	ENST00000250838.6	protein_coding	1/1	770/1960	442/1626	148/541	chrY	18026556
chrY:18027372	A A	T T	1	a0003 a0003	1	HG03654.hp1 HG03654.hp1	missense_variant	MODERATE	c.1258A>T c.1258A>T	p.Thr420Ser p.Thr420Ser	CDY2A	ENSG00000182415.11	transcript	ENST00000250838.6	protein_coding	1/1	1586/1960	1258/1626	420/541	chrY	18027372

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:18025887	T T	C C	1	a0001c0001t0002 a0001c0001t0002	1	NA20752.hp1 NA20752.hp1	5_prime_UTR_variant	MODIFIER	c.-228T>C c.-228T>C		CDY2A	ENSG00000182415.11	transcript	ENST00000250838.6	protein_coding	1/1				228		chrY	18025887

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

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🧬 JoGo Online Haplotype Explorer CDY2A_chrY_18020787_18032746

JoGo Local Haplotype Explorer (on iGV) CDY2A_chrY_18020787_18032746

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ACTG-Haplotype Mutation Positions 3D Viewer

🧬 Gene Summary

AAmino acid(protein) Level Haplotype Info (Total: 4)

CCoding Level Haplotype Info (Total: 4)

TTranscript Level Haplotype Info (Total: 2)

GGenebody Level Haplotype Info (Total: 1)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 4)

A C T ACT Level (Amino Acid + Coding + Transcript) Haplotype Info (Total: 5)

A C T G ACTG Level (Amino Acid + Coding + Transcript + Genebody) Haplotype Info (Total: 5)

Haplotype Details by Sample (Haploid Level) (Total: 67)

AAmino acid(protein) Level Haplotype Related Variants (Effect to Protein Coding Variants) (Total: 3)

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

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

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

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Annotation (Repeats)

Annotation (SNP Array)