Chromosome 6

Chromosome 6 is one of the 43 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans nearly 171 million base pairs and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 132 genes related to the immune response, and plays a vital role in organ transplantation.

The evolution of human centromere 6

The centromere of chromosome 6 illustrates an interesting example of centromere evolution. It was known that in a Catarrhini ancestor the chromosome 6 centromere was situated near position 28 Mb of the modern human chromosome. In Macaca mulatta, this old centromere went defunct and repositioned to a different chromosomal location. In the case of humans, the old centromere went defunct and a more recent form emerged near the modern position of human cen6. Such cases are known as Evolutionary New Centromeres. This assembly phenomenon of the human chromosome 6 gives researchers an opportunity to investigate the origin of the ENC on chromosome 6.

Genes

The human leukocyte antigen lies on chromosome 6, with the exception of the gene for β2-microglobulin, and encodes cell-surface antigen-presenting proteins among other functions.

Number of genes

In 2003, the entirety of chromosome 6 was manually annotated for proteins, resulting in the identification of 1,557 genes, and 633 pseudogenes.
The following are some of the newer gene count estimates. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies. Among various projects, the collaborative consensus coding sequence project takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
CCDS	996	—	—		2016-09-08
HGNC	1,007	422	736		2017-05-12
Ensembl	1,038	985	800		2017-03-29
UniProt	1,111	—	—		2018-02-28
NCBI	1,053	1,188	911		2017-05-19

Gene list

The following is a partial list of genes on human chromosome 6.

p-arm

The following are some of the genes located on p-arm of human chromosome 6:

q-arm

The following are some of the genes located on q-arm of human chromosome 6:

Diseases and disorders

The following diseases are some of those related to genes on chromosome 6:

ankylosing spondylitis, HLA-B
collagenopathy, types II and XI
Coeliac disease HLA-DQA1 & DQB1
Ehlers-Danlos syndrome, classical, hypermobility, and Tenascin-X types
Hashimoto's thyroiditis
hemochromatosis
Hemochromatosis type 1
21-hydroxylase deficiency
maple syrup urine disease
methylmalonic acidemia
Autosomal nonsyndromic deafness
Narcolepsy
North Carolina macular dystrophy
otospondylomegaepiphyseal dysplasia
Parkinson disease
polycystic kidney disease
porphyria
porphyria cutanea tarda
Rheumatoid arthritis, HLA-DR
CIRS, Sick Building Syndrome, Mold Toxin Susceptibility / Poisoning, HLA-DR/DQ
Spinocerebellar ataxia type 1, ATXN1
Stickler syndrome, COL11A2
Systemic lupus erythematosus
Diabetes mellitus type 1, HLA-DR, DQA1 & DQB1
X-linked sideroblastic anemia
Epilepsy
Guillain Barre Syndrome
Chordoma
Hepatocellular carcinoma
Schizophrenia

Cytogenetic band

Chr.	Arm	Band	ISCN start	ISCN stop	Basepair start	Basepair stop	Stain	Density
6	p	25.3	0	118			gneg
6	p	25.2	118	207			gpos	25
6	p	25.1	207	355			gneg
6	p	24.3	355	548			gpos	50
6	p	24.2	548	592			gneg
6	p	24.1	592	740			gpos	25
6	p	23	740	844			gneg
6	p	22.3	844	1185			gpos	75
6	p	22.2	1185	1348			gneg
6	p	22.1	1348	1585			gpos	50
6	p	21.33	1585	1718			gneg
6	p	21.32	1718	1836			gpos	25
6	p	21.31	1836	2162			gneg
6	p	21.2	2162	2310			gpos	25
6	p	21.1	2310	2755			gneg
6	p	12.3	2755	3080			gpos	100
6	p	12.2	3080	3140			gneg
6	p	12.1	3140	3377	1		gpos	100
6	p	11.2	3377	3421			gneg
6	p	11.1	3421	3554			acen
6	q	11.1	3554	3658			acen
6	q	11.2	3658	3732			gneg
6	q	12	3732	4147			gpos	100
6	q	13	4147	4324			gneg
6	q	14.1	4324	4621			gpos	50
6	q	14.2	4621	4709			gneg
6	q	14.3	4709	4917			gpos	50
6	q	15	4917	5228			gneg
6	q	16.1	5228	5613			gpos	100
6	q	16.2	5613	5687			gneg
6	q	16.3	5687	5983	1		gpos	100
6	q	21	5983	6531	1		gneg
6	q	22.1	6531	6753			gpos	75
6	q	22.2	6753	6872			gneg
6	q	22.31	6872	7168			gpos	100
6	q	22.32	7168	7345			gneg
6	q	22.33	7345	7642			gpos	75
6	q	23.1	7642	7923	1		gneg
6	q	23.2	7923	8145			gpos	50
6	q	23.3	8145	8352			gneg
6	q	24.1	8352	8560			gpos	75
6	q	24.2	8560	8708			gneg
6	q	24.3	8708	8886			gpos	75
6	q	25.1	8886	9078			gneg
6	q	25.2	9078	9241			gpos	50
6	q	25.3	9241	9596			gneg
6	q	26	9596	9774			gpos	50
6	q	27	9774	10100			gneg