Evidence · Replicated

What the research found

In the cited research, the A allele at rs2090409 was associated with earlier timing of the first menstrual period in studied women.

CC: Later
AC: Middle
AA: Earlier

Slight effect

What the study found

In the study, each copy went with age at the first menstrual period about 4.7 weeks lower on average.

Women of European descent: up to 87,802 in 32 discovery studies and up to 14,731 in 16 replication studies · Table 1, rs2090409 row ('Previous menarche loci'); beta defined in footnote g as the per-allele change in weeks from Stage 1 + Replication

Evidence: Genome-wide association with independent replication
Who was studied: Women of European descent

The research behind this card was done only in women, so it is part of a report requested as female.

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	CCLater	ACMiddle	AAEarlier
All regions2,504 people	47%	42%	11%
Africa661 people	42%	45%	14%
The Americas347 people	41%	49%	10%
East Asia504 people	35%	47%	18%
Europe503 people	46%	44%	11%
South Asia489 people	71%	27%	2%

Among the 2,504 people of the 1000 Genomes Project, in five world regions. These percentages describe groups of people, never anyone’s chance of having a trait.

Ancient genomes

Through time

How often the studied letter was read in ancient people, era by era, in the region chosen.

Region

Through time: Europe
Before farmingbefore 6500 BC	20%12 of 59 copies read
First farmers6500 to 3000 BC	33%162 of 487 copies read
Bronze Age3000 to 1200 BC	23%87 of 381 copies read
Iron Age and Antiquity1200 BC to AD 600	32%270 of 850 copies read
Middle AgesAD 600 to 1500	31%323 of 1,034 copies read
Today1000 Genomes	33%329 of 1,006 copies

Neanderthal and Denisovan genomes

Altai Neanderthal: 2 copies
Vindija Neanderthal: 2 copies
Chagyrskaya Neanderthal: 2 copies
Denisovan: 2 copies

Neanderthals and Denisovans carried this letter too: it is the older of the two.

For most ancient people only one of their two copies can be read, so these counts are copies read, not people. Close relatives, repeated samples and samples the archive marks as unreliable are left out. Ancient genomes from the Allen Ancient DNA Resource (AADR v66): 15,136 people.

rs2090409

The marker

Gene or region: 9q31.2 region (near TMEM38B)
Marker: rs2090409
Location: Chromosome 9 · GRCh37 108,967,088 · GRCh38 106,204,807
Letters studied: A and C, with A as the studied allele

A DNA Traits report reads this marker in your raw DNA file and shows which of the three genotypes is yours, with how common it is. It counts the copies of the studied allele; it does not measure the trait itself.

Marker: 9q31.2 region (near TMEM38B) · rs2090409
Location: Chromosome 9 · GRCh37 108,967,088 · GRCh38 106,204,807
Studied allele: A
Published statistic: beta -4.7 weeks per A allele (SE 0.4), P 2.2e-33 (Stage 1 + replication); replication alone P 2.7e-6 in 14,708 women; A frequency 0.31; direction -/- in both stages (Elks 2010 Table 1) (Table 1, rs2090409 row ('Previous menarche loci'); beta defined in footnote g as the per-allele change in weeks from Stage 1 + Replication)
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 1171 / 1051 / 282 · Africa 276 / 295 / 90 · The Americas 141 / 171 / 35 · East Asia 178 / 236 / 90 · Europe 229 / 219 / 55 · South Asia 347 / 130 / 12

See this card in the sample report

Limits

What it cannot tell you

Studied in women of European descent who recalled their age at the first period. A single marker, one of more than a hundred linked to its timing.

Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies (Elks et al., 2010)

The same topic

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