Joint Open Genome and Omics Platform (JoGo)

Search by Genic region

geneid	353144
ensemblid	ENSG00000244057.5
hgncid	16612
symbol	LCE3C
name	late cornified envelope 3C
refseq_nuc	NM_178434.3
refseq_prot	NP_848521.1
ensembl_nuc	ENST00000684028.1
ensembl_prot	ENSP00000507204.1
mane_status	MANE Select
chr	chr1
start	152600234
end	152601086
strand	+
ver	v1.2
region	chr1:152600234-152601086
region5000	chr1:152595234-152606086
regionname0	LCE3C_chr1_152600234_152601086
regionname5000	LCE3C_chr1_152595234_152606086

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	1/1	94	53	23	4	20	2	2	18	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0002	0/0	94	3	3	0	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0003	0/0	94	2	2	0	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086

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	1/1	285	53	23	4	20	2	2	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
c0002	0/0	285	3	3	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
c0003	0/0	285	2	2	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086

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	1/1	147	58	28	4	20	2	2	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086

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
g0001	1/1	57	28	4	20	1	2	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
g0002	0/0	1	0	0	0	1	0	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086

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	1/1	285	53	23	4	20	2	2	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0002c0002	0/0	285	3	3	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0003c0003	0/0	285	2	2	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	1/1	431	53	23	4	20	2	2	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0002c0002t0001	0/0	431	3	3	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086
a0003c0003t0001	0/0	431	2	2	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	copy fasta	chr1	152595234	152606086

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
a0001c0001t0001g0001	1/1	52	23	4	20	1	2	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
a0001c0001t0001g0002	0/0	1	0	0	0	1	0	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
a0002c0002t0001g0001	0/0	3	3	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
a0003c0003t0001g0001	0/0	2	2	0	0	0	0	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00323	hp1	a0001	c0001	t0001	g0001	EUR	FIN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG00323	hp2	a0001	c0001	t0001	g0002	EUR	FIN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG01496	hp1	a0001	c0001	t0001	g0001	AMR	CLM	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG01496	hp2	a0001	c0001	t0001	g0001	AMR	CLM	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG01975	hp1	a0001	c0001	t0001	g0001	AMR	PEL	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG01975	hp2	a0001	c0001	t0001	g0001	AMR	PEL	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02055	hp1	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02055	hp2	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02258	hp1	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02258	hp2	a0002	c0002	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02451	hp1	a0003	c0003	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02451	hp2	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02717	hp1	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02717	hp2	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02886	hp1	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02886	hp2	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02922	hp1	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02922	hp2	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02976	hp1	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02976	hp2	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03041	hp1	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03041	hp2	a0001	c0001	t0001	g0001	AFR	GWD	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03098	hp1	a0003	c0003	t0001	g0001	AFR	MSL	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03098	hp2	a0001	c0001	t0001	g0001	AFR	MSL	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03195	hp1	a0002	c0002	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03195	hp2	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03516	hp1	a0001	c0001	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG03516	hp2	a0002	c0002	t0001	g0001	AFR	ESN	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG04115	hp1	a0001	c0001	t0001	g0001	SAS	STU	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG04115	hp2	a0001	c0001	t0001	g0001	SAS	STU	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18747	hp1	a0001	c0001	t0001	g0001	EAS	CHB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18747	hp2	a0001	c0001	t0001	g0001	EAS	CHB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18906	hp1	a0001	c0001	t0001	g0001	AFR	YRI	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18906	hp2	a0001	c0001	t0001	g0001	AFR	YRI	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18953	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18953	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18968	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18968	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18983	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18983	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18985	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18985	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18997	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA18997	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19003	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19003	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19043	hp1	a0001	c0001	t0001	g0001	AFR	LWK	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19043	hp2	a0001	c0001	t0001	g0001	AFR	LWK	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19058	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19058	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19065	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19065	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19089	hp1	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
NA19089	hp2	a0001	c0001	t0001	g0001	EAS	JPT	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02486	hp1	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
HG02486	hp2	a0001	c0001	t0001	g0001	AFR	ACB	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
homoSapiens_chm13v2	hp1	a0001	c0001	t0001	g0001	REF	REF	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086
homoSapiens_grch38	hp1	a0001	c0001	t0001	g0001	REF	REF	LCE3C_chr1_152595234_152606086	LCE3C	chr1	152595234	152606086

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
chr1:152600987	C C	T T	1	a0002 a0002	3	HG02258.hp2 HG03195.hp1 HG03516.hp2 HG02258.hp2 HG03195.hp1 HG03516.hp2	missense_variant	MODERATE	c.256C>T c.256C>T	p.Arg86Cys p.Arg86Cys	LCE3C	ENSG00000244057.5	transcript	ENST00000684028.1	protein_coding	2/2	332/431	256/285	86/94			chr1	152600987
chr1:152600988	G G	A A	1	a0003 a0003	2	HG02451.hp1 HG03098.hp1 HG02451.hp1 HG03098.hp1	missense_variant	MODERATE	c.257G>A c.257G>A	p.Arg86His p.Arg86His	LCE3C	ENSG00000244057.5	transcript	ENST00000684028.1	protein_coding	2/2	333/431	257/285	86/94			chr1	152600988

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

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
chr1:152600565	C C	T T	1	a0001c0001t0001g0002 a0001c0001t0001g0002	1	HG00323.hp2 HG00323.hp2	intron_variant	MODIFIER	c.-25-142C>T c.-25-142C>T		LCE3C	ENSG00000244057.5	transcript	ENST00000684028.1	protein_coding	1/1						chr1	152600565

Search by Genic region

Search

🧬 JoGo Online Haplotype Explorer LCE3C_chr1_152595234_152606086

JoGo Local Haplotype Explorer (on iGV) LCE3C_chr1_152595234_152606086

Translation Multiple Alignment View

🧬 Gene Summary

AAmino acid(protein) Level Haplotype Info (Total: 3)

CCoding Level Haplotype Info (Total: 3)

TTranscript Level Haplotype Info (Total: 1)

GGenebody Level Haplotype Info (Total: 2)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 3)

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: 4)

Haplotype Details by Sample (Haploid Level) (Total: 58)

AAmino acid(protein) Level Haplotype Related Variants (Effect to Protein Coding Variants) (Total: 2)

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

TTranscript Level Haplotype Variants (5'UTR+3'UTR) (Total: 0)

GGenebody Level Haplotype Variants (Intron) (Total: 1)

External Link

Annotation (Repeats)

Annotation (SNP Array)