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regulomedb.md

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1# RegulomeDB

3Regulatory evidence for **noncoding** SNVs: ENCODE TF ChIP, DNase, motifs,

4QTLs. Rank `1a` (strongest) through `7` (nothing overlapping). Neighbour of

5`encode.md` and `jaspar.md`. Not a consequence scorer — for missense impact

6use Ensembl VEP (`ensembl.md` §6, `CADD=1`).

8Search: `https://regulomedb.org/regulome-search/`

9Help: https://regulomedb.org/regulome-help/

10The `rs6983267` GET response was rechecked on 2026-09-30. Other numeric examples below are historical observations from 2026-09-10, not current guarantees.

RegulomeDB

Regulatory evidence for noncoding SNVs: ENCODE TF ChIP, DNase, motifs, QTLs. Rank 1a (strongest) through 7 (nothing overlapping). Neighbour of encode.md and jaspar.md. Not a consequence scorer — for missense impact use Ensembl VEP (ensembl.md §6, CADD=1).

Search: https://regulomedb.org/regulome-search/ Help: https://regulomedb.org/regulome-help/ The rs6983267 GET response was rechecked on 2026-09-30. Other numeric examples below are historical observations from 2026-09-10, not current guarantees.

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12## Request

14```

15GET /regulome-search/?regions={rsID|chr:start-end}&genome=GRCh38&format=json

16```

18`genome` is `GRCh38` (preferred) or `GRCh37`. Default format is HTML.

20Coordinates are **0-based half-open**, same as BED. A single GRCh38 base

21at 1-based position `P` is `chrN:{P-1}-{P}`.

Request

GET /regulome-search/?regions={rsID|chr:start-end}&genome=GRCh38&format=json

genome is GRCh38 (preferred) or GRCh37. Default format is HTML.

Coordinates are 0-based half-open, same as BED. A single GRCh38 base at 1-based position P is chrN:{P-1}-{P}.

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23## Verified calls

25```

26GET ...?regions=rs6983267&genome=GRCh38&format=json

27```

29`regulome_score.ranking` **1a**, `probability` **0.93**. This is the

30example of a regulatory hit.

32```

33GET ...?regions=rs28934578&genome=GRCh38&format=json

34GET ...?regions=chr17:7675087-7675088&genome=GRCh38&format=json

35```

37Both: ranking **4**, probability **0.60906**. A coding missense with rank

384 is "not what this database is for," not "benign regulatory."

40```

41GET ...?regions=chr17:7674220-7674220&genome=GRCh38&format=json

42```

44HTTP 200, `variants: []`, no `regulome_score.ranking`. Zero-width /

451-based same-number ranges miss the base.

47```

48POST /regulome-search/ with a JSON body

49```

51HTTP 200, `@id` `/regulome-notfound`, `@type` includes `regulome-help`.

52That historical POST probe did not return search results. Use the documented GET search; an HTTP 200 alone does not establish a valid result.

Verified calls

GET ...?regions=rs6983267&genome=GRCh38&format=json

regulome_score.ranking 1a, probability 0.93. This is the example of a regulatory hit.

GET ...?regions=rs28934578&genome=GRCh38&format=json
GET ...?regions=chr17:7675087-7675088&genome=GRCh38&format=json

Both: ranking 4, probability 0.60906. A coding missense with rank 4 is "not what this database is for," not "benign regulatory."

GET ...?regions=chr17:7674220-7674220&genome=GRCh38&format=json

HTTP 200, variants: [], no regulome_score.ranking. Zero-width / 1-based same-number ranges miss the base.

POST /regulome-search/   with a JSON body

HTTP 200, @id /regulome-notfound, @type includes regulome-help. That historical POST probe did not return search results. Use the documented GET search; an HTTP 200 alone does not establish a valid result.

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54## Traps

56- Convert 1-based VEP/CADD positions before building `regions=`.

57- Read `regulome_score.ranking`, not a legacy `regulomedb_score` field.

58- `probability` is a string.

59- Region queries without an rsID return common SNPs (MAF > 1%) in the

60 window, not every possible SNV.

61- Rank 7 / missing ranking is "no annotated overlap," not a proof the

62 variant does nothing.

Traps

Convert 1-based VEP/CADD positions before building regions=.
Read regulome_score.ranking, not a legacy regulomedb_score field.
probability is a string.
Region queries without an rsID return common SNPs (MAF > 1%) in the window, not every possible SNV.
Rank 7 / missing ranking is "no annotated overlap," not a proof the variant does nothing.

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