D1S1656

CODIS Core

D1S1656 is a tetranucleotide short tandem repeat (STR) locus on chromosome 1 (1q42.2), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

1q42.2

STRNaming template (FSSG)

AC[n]CTAT[n]

Type

Tetranucleotide

Alternative motifs (STRbase, historical notation)

[TCTA]n, CCTA [TCTA]n TCA [TCTA]n, CTTA [TCTA]n

Reference Allele

Explore internal sequence structure

See how the STRNaming name of the reference allele maps onto its sequence: repeat blocks, flanking regions and flanking variants.

Open STR Motif Explorer

See the reads at this locus

Open the built-in IGV viewer on the hg38 window of this marker with a 1000 Genomes sample.

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Genomic Coordinates

GRCh38/hg38

Repeat region

chr1:230,769,616-230,769,683 (68 bp)

GRCh37/hg19

Repeat region

chr1:230,905,362-230,905,429 (68 bp)

Motif and sequences are shown on the forward (+) strand of GRCh38.

Sequence structure (FSSG)

ISFG minimum range, bracketing and kit coverage from the Forensic Sequence Structure Guide, FSSG v6.1 (STRidER; distributed as FSSG_v6-1_beta.xlsx).

STRNaming Formatted ISFG Minimum Range for Common Alleles (FSSG)

AC[n]CTAT[n]

AC[n]AT[1]CTAT[n]

AC[n]CTAT[n]CAT[1]CTAT[n]

AC[n]AT[1]CTAT[n]CAT[1]CTAT[n]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE17_AC[6]CTAT[16]

Historical bracketing (2016-2023)

CCTA [TCTA]16

ISFG minimum range (GRCh38)

chr1:230,769,601-230,769,687 (87 bp)

MPS kits covering this locus

PowerSeq 46GY
ForenSeq Signature Prep/Plus and MainstAY (Does not cover the whole ISFG minimum range.)
Precision ID GlobalFiler NGS STR Panel v2
IDSeek OmniSTR Global

Kit range does not cover the whole ISFG minimum range of this locus (chr1:230,769,601-230,769,687), according to the kit ranges in the FSSG. Bases of the minimum range outside a kit's range are not sequenced by that kit; bases filled in from the reference should be identified as such.

Notes from the FSSG

ForenSeq MainstAY/Signature Prep range shown is exclusive of primer, inferred bases may be included in UAS output.

Allele frequencies at a glance

Most common allele per population group, with its frequency and the sample size, in the capillary electrophoresis data of pop.STR / SP-SMART.

Africa: Allele 14 (0.225, n = 102)
Native American: Allele 14 (0.175, n = 548)
East Asia: Allele 15 (0.278, n = 225)
Central and South Asia: Allele 15 (0.191, n = 199)
Europe: Allele 15 (0.162, n = 1,817)
Middle East: Allele 16 (0.209, n = 151)
Oceania: Allele 16 (0.271, n = 24)

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.
Allele	AFR	NAM	EAS	CSA	EUR	MES	OCE
8	0	0	0	0.013	0	0	0
9	0	0	0	0.010	0	0	0
10	0.025	0.003	0.002	0.013	0.006	0.003	0
11	0.059	0.059	0.060	0.126	0.053	0.076	0.063
12	0.049	0.089	0.051	0.083	0.093	0.126	0.063
13	0.172	0.090	0.098	0.116	0.088	0.086	0.104
13.3	0.005	0	0	0	0	0	0
14	0.225	0.175	0.071	0.101	0.137	0.093	0.083
14.3	0.010	0.016	0.002	0	0.004	0	0
15	0.137	0.141	0.278	0.191	0.162	0.152	0.083
15.3	0.010	0.033	0	0.013	0.045	0.043	0.021
16	0.147	0.134	0.220	0.166	0.147	0.209	0.271
16.3	0.083	0.059	0.007	0.038	0.061	0.053	0
17	0.044	0.045	0.089	0.050	0.046	0.073	0.208
17.1	0	0.001	0	0	0	0	0
17.3	0.025	0.105	0.064	0.050	0.108	0.060	0.021
18	0	0.006	0.011	0.008	0.007	0.003	0.063
18.3	0.010	0.036	0.038	0.020	0.036	0.017	0
19	0	0.001	0	0	0	0	0
19.3	0	0.006	0.009	0.005	0.007	0.007	0.021

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.

Variant Alleles

STRbase reports 58 sequence variants across 23 allele designations.

13.3

14.3

15.3

16.1

16.3

17.1

17.3

18.3

19.3

20.3

Related markers

Other STR markers on chromosome 1

D1S1677

Other CODIS core loci

Browse the full STR marker catalog