GPN-MSA
Collection
https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1
•
8 items
•
Updated
chrom
large_stringlengths 1
2
| pos
int64 10.4k
249M
| ref
large_stringlengths 1
1
| alt
large_stringlengths 1
1
| label
bool 2
classes | consequence
large_stringlengths 5
25
| GPN-MSA
float32 -12.11
10.7
| CADD
float32 -8.77
1.95
| phyloP-100v
float64 -9.89
15.7
⌀ | phyloP-241m
float64 -9.19
20
⌀ | phastCons-100v
float64 -1
-0
⌀ | NT
float32 -10.61
9.66
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 13,273 | G | C | false | ncRNA | -4.074219 | -0.398596 | -1.091 | -0.864 | -1 | 0.11441 |
1 | 14,464 | A | T | false | ncRNA | 0.89502 | 0.339809 | 1.705 | -0.992 | -0 | -0.155609 |
1 | 16,688 | G | A | false | ncRNA | -4.027344 | -1.448712 | -3.121 | -1.305 | -0.996 | -1.57756 |
1 | 17,697 | G | C | false | ncRNA | -4.734375 | -1.043489 | -2.491 | -8.751 | -1 | 0.863495 |
1 | 49,554 | A | G | false | Enhancer | -1.988281 | -0.227302 | -0.024 | 0.078 | -0.003 | null |
1 | 51,479 | T | A | false | Promoter | -1.28125 | -0.208313 | 0.212 | -0.604 | -0.001 | -2.320801 |
1 | 51,803 | T | C | false | Promoter | -1.322266 | -0.448316 | -0.393 | -0.107 | -0.091 | -3.083298 |
1 | 51,928 | G | A | false | Promoter | 1.206055 | -0.244843 | -0.176 | 0.06 | -0.001 | 0.418243 |
1 | 52,058 | G | C | false | Promoter | -1.276367 | 0.07386 | 0.238 | -0.137 | -0 | -0.945038 |
1 | 52,238 | T | G | false | Promoter | 1.34375 | 0.04854 | 1.025 | -0.078 | -0 | 1.140945 |
1 | 54,366 | A | G | false | Enhancer | -1.580078 | -0.252664 | -0.289 | -0.107 | -0.067 | null |
1 | 54,380 | T | C | false | Enhancer | -1.324219 | -0.529307 | 0.018 | 0.162 | -0 | null |
1 | 54,421 | A | G | false | Enhancer | 1.257813 | -0.02868 | 0.568 | -0.333 | -0.001 | null |
1 | 54,490 | G | A | false | Enhancer | 0.039063 | 0.201295 | 0.313 | -0.029 | -0 | null |
1 | 54,586 | T | C | false | Enhancer | 0.9375 | -0.178471 | 0.549 | 0.213 | -0 | null |
1 | 54,676 | C | T | false | Enhancer | 3.912109 | -0.059604 | 0.086 | -0.285 | -0.007 | null |
1 | 54,844 | G | A | false | Enhancer | -1.818359 | -0.160976 | -0.514 | -0.527 | -0.004 | null |
1 | 55,164 | C | A | false | Enhancer | 1.34375 | 0.538769 | 2.152 | 1.826 | -0 | null |
1 | 55,545 | C | T | false | Enhancer | 1.870117 | -0.295491 | -0.696 | 0.768 | -0.007 | null |
1 | 55,926 | T | C | false | Enhancer | -1.318359 | 0.20604 | 0.999 | 0.271 | -0 | null |
1 | 58,771 | T | C | false | ncRNA | -5.105469 | -1.633646 | -1.161 | -0.426 | -0.797 | -1.934265 |
1 | 63,268 | T | C | false | ncRNA | -2.367188 | 0.038139 | -0.486 | -0.436 | -0 | -3.040726 |
1 | 63,516 | A | G | false | ncRNA | -2.964844 | -1.075005 | -0.029 | 0.093 | -0 | -2.457718 |
1 | 63,527 | T | C | false | ncRNA | 0.306152 | -0.163349 | 1.32 | -0.619 | -0 | -1.642197 |
1 | 63,671 | G | A | false | ncRNA | 3.130859 | -0.344458 | 1.392 | -0.253 | -0 | 2.005463 |
1 | 63,697 | T | C | false | ncRNA | -6.382813 | -1.180623 | -1.155 | -2.212 | -0.701 | -4.765289 |
1 | 64,025 | T | C | false | ncRNA | -1.170898 | -0.398742 | -0.081 | -0.51 | -0 | -0.320374 |
1 | 64,764 | C | T | false | Promoter | 1.634766 | -0.268436 | -0.249 | -0.404 | -0 | 3.997162 |
1 | 64,931 | G | A | false | Promoter | -0.954102 | -0.062455 | 0.527 | 1.044 | -0 | 1.722168 |
1 | 73,649 | C | G | false | Enhancer | -2.121094 | -0.451789 | -0.264 | 0.267 | -0.316 | null |
1 | 75,767 | G | A | false | Enhancer | 0.196289 | -0.115283 | null | -0.086 | null | null |
1 | 76,057 | A | G | false | Enhancer | -2.160156 | -0.248493 | null | -0.071 | null | null |
1 | 76,206 | T | C | false | Enhancer | -0.300293 | -0.244829 | null | -0.072 | null | null |
1 | 76,240 | A | G | false | Enhancer | -0.107422 | -0.269503 | null | -0.071 | null | null |
1 | 76,838 | T | G | false | Enhancer | -0.165527 | -0.107129 | 1.366 | 1.26 | -0.02 | null |
1 | 76,854 | A | G | false | Enhancer | 0.055176 | -0.489965 | -0.153 | -0.399 | -0.053 | null |
1 | 77,089 | C | T | false | Enhancer | 1.47168 | -0.415083 | -0.136 | 0.304 | -0.05 | null |
1 | 77,866 | C | T | false | Enhancer | 0.369629 | -0.641195 | -0.136 | -0.323 | -0.313 | null |
1 | 77,961 | G | A | false | Enhancer | 2.628906 | -0.10487 | 1.236 | 0.614 | -0.077 | null |
1 | 79,772 | C | G | false | Enhancer | -0.030762 | -0.138785 | -0.178 | -0.323 | -0.011 | null |
1 | 80,323 | G | C | false | Enhancer | 0.372559 | -0.451047 | -0.196 | 0.663 | -0.183 | null |
1 | 80,619 | G | A | false | Enhancer | 0.577148 | -0.207171 | -0.196 | -0.294 | -0.015 | null |
1 | 80,857 | C | T | false | Enhancer | 1.063477 | -0.339268 | -0.147 | -0.268 | -0.004 | null |
1 | 81,260 | C | T | false | Enhancer | -0.041992 | 0.073795 | 1.311 | 0.296 | -0.002 | null |
1 | 81,343 | A | G | false | Enhancer | -2.310547 | -0.233605 | -0.165 | 0.415 | -0.051 | null |
1 | 82,163 | G | A | false | Enhancer | 2.882813 | -0.124033 | -0.173 | -0.531 | -0.062 | null |
1 | 82,400 | G | A | false | Enhancer | 2.724609 | -0.125267 | -0.173 | -0.293 | -0.026 | null |
1 | 82,562 | T | C | false | Enhancer | 0.079102 | -0.234119 | -0.148 | -0.231 | -0.023 | null |
1 | 82,609 | C | G | false | Enhancer | 0.246094 | -0.044349 | -0.147 | -0.295 | -0.013 | null |
1 | 82,676 | T | G | false | Enhancer | -0.427246 | -0.580291 | -0.148 | -0.237 | -0.33 | null |
1 | 82,734 | T | C | false | Enhancer | 0.005859 | -0.228981 | 1.694 | 0.658 | -0.031 | null |
1 | 83,084 | T | A | false | Enhancer | 0.756836 | -0.016189 | 1.858 | 2.321 | -0.027 | null |
1 | 83,443 | C | T | false | Enhancer | -0.074219 | -0.79636 | -0.147 | -0.087 | -0.352 | null |
1 | 83,795 | G | A | false | Enhancer | -0.011719 | -0.052672 | 1.713 | 1.999 | -0.004 | null |
1 | 84,002 | G | A | false | Enhancer | 0.780273 | -0.016299 | -0 | -0 | -0.022 | null |
1 | 84,244 | A | C | false | Enhancer | -0.757324 | -0.049621 | -0.117 | -0.052 | -0.312 | null |
1 | 84,307 | C | A | false | Enhancer | 0.730957 | 0.075284 | 2.015 | 2.345 | -0.046 | null |
1 | 84,683 | A | G | false | Enhancer | -0.541992 | -0.230736 | 1.755 | 2.119 | -0.029 | null |
1 | 85,529 | G | A | false | Enhancer | 2.621094 | -0.232815 | 1.711 | 0.801 | -0.175 | null |
1 | 85,597 | A | C | false | Enhancer | -1.033203 | -0.552093 | -0.127 | -0.25 | -0.34 | null |
1 | 86,018 | C | G | false | Enhancer | 0.283203 | -0.01549 | 2.28 | 2.175 | -0.061 | null |
1 | 86,065 | G | C | false | Enhancer | -0.060547 | 0.014888 | -0.286 | -0.017 | -0.018 | null |
1 | 86,303 | G | T | false | Enhancer | 0.916992 | 0.114918 | 0.851 | 0.493 | -0.012 | null |
1 | 86,331 | A | G | false | Enhancer | -0.48877 | -0.167432 | -0.272 | -0.731 | -0.044 | null |
1 | 87,190 | G | A | false | Enhancer | -1.007813 | -0.048625 | 1.499 | 2.304 | -0.005 | null |
1 | 88,136 | G | A | false | Enhancer | -1.449219 | -0.215278 | -0.438 | -0.317 | -0.005 | null |
1 | 88,169 | C | T | false | Enhancer | -2.121094 | -0.194336 | -0.371 | 0.702 | -0.038 | null |
1 | 88,172 | G | A | false | Enhancer | 1.052734 | -0.170995 | -0.438 | 1.578 | -0.027 | null |
1 | 88,177 | G | C | false | Enhancer | -3.109375 | -0.146098 | -0.438 | -0.322 | -0.023 | null |
1 | 89,599 | A | T | false | ncRNA | -0.11084 | -0.198045 | -0.117 | 0.019 | -0.566 | 1.741074 |
1 | 89,946 | A | T | false | ncRNA | -0.108887 | -0.170372 | -0.117 | 0.855 | -0.035 | -2.520203 |
1 | 90,007 | G | A | false | ncRNA | -1.070313 | -0.155082 | -0.123 | -0.491 | -0.197 | -3.06636 |
1 | 91,190 | G | A | false | ncRNA | 1.584961 | -0.247392 | -0.123 | 1.199 | -0.065 | -0.367081 |
1 | 91,421 | T | C | false | ncRNA | -1.962891 | -0.506171 | 1.639 | 2.426 | -0.261 | -1.994446 |
1 | 91,605 | C | T | false | ncRNA | 0.30127 | -0.311057 | -0.105 | -0.865 | -0.044 | 0.039276 |
1 | 131,310 | G | C | false | ncRNA | -2.480469 | -0.227829 | -0.679 | -6.959 | -0.002 | -0.085175 |
1 | 133,160 | G | A | false | ncRNA | -0.618164 | -0.173938 | 0.488 | -1.779 | -0 | -0.972931 |
1 | 133,483 | G | T | false | ncRNA | -1.40918 | -0.139635 | -1.097 | 3.213 | -0.005 | 2.053314 |
1 | 136,437 | T | C | false | Promoter | -0.912598 | -0.454278 | 2.884 | -0 | -0 | 4.047104 |
1 | 136,635 | T | G | false | Promoter | 1.493164 | -0.687213 | 0.24 | -0 | -0 | -5.361816 |
1 | 136,817 | T | C | false | Promoter | 0.622559 | -0.775266 | 2.258 | -0 | -0 | -6.990189 |
1 | 137,825 | G | A | false | ncRNA | 0.962402 | -0.320727 | 0.026 | null | -0.001 | -1.20256 |
1 | 138,593 | G | T | false | Promoter | -1.613281 | -0.08484 | -0.436 | null | -0.008 | -3.858597 |
1 | 181,321 | C | G | false | Enhancer | 0.117188 | -0.501456 | null | -0.076 | null | null |
1 | 181,583 | C | G | false | Enhancer | -0.749023 | -0.469966 | null | -0.092 | null | null |
1 | 181,706 | G | A | false | Promoter | -0.556152 | -0.434034 | null | -0.091 | null | -1.906433 |
1 | 183,800 | C | G | false | ncRNA | -5.15625 | -0.875078 | -6.08 | -4.848 | -0.949 | 0.199371 |
1 | 185,497 | G | A | false | ncRNA | -3.074219 | -1.825089 | -1.285 | -4.388 | -0.995 | -0.233536 |
1 | 187,153 | T | C | false | ncRNA | -2.976563 | -0.430129 | -0.258 | 1.506 | -0.018 | -1.609665 |
1 | 187,259 | G | T | false | ncRNA | 1.665039 | 0.607216 | 5.309 | 20 | -0 | 1.677856 |
1 | 188,252 | G | T | false | ncRNA | -4.585938 | -0.983406 | -1.126 | -2.935 | -1 | -1.500809 |
1 | 202,330 | C | A | false | Enhancer | -1.375 | -0.763342 | 0.171 | -0.868 | -0 | null |
1 | 206,074 | T | C | false | Enhancer | 1.161133 | -0.530138 | 0.168 | 0.374 | -0 | null |
1 | 206,849 | C | G | false | Enhancer | -2.746094 | -0.431993 | -0.038 | -0.435 | -0.001 | null |
1 | 206,863 | T | C | false | Enhancer | 3.609375 | -1.287873 | -0.84 | -2.68 | -0.646 | null |
1 | 206,930 | G | A | false | Enhancer | 3.951172 | -1.07014 | -0.231 | -0.577 | -0.991 | null |
1 | 263,722 | C | G | false | ncRNA | 0.079102 | 0.263589 | 2.308 | -0.586 | -0 | -2.308746 |
1 | 264,481 | G | A | false | ncRNA | 1.994141 | -0.15525 | 1.718 | 1.218 | -0.001 | 3.506775 |
1 | 264,557 | A | G | false | ncRNA | 0.164063 | -0.399896 | 0.643 | 0.181 | -0 | 0.392944 |
1 | 264,562 | C | T | false | ncRNA | 0.09375 | -0.150344 | 0.781 | 0.249 | -0.001 | 0.075928 |
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OMIM variants
For more information check out our paper and repository.
Usage
- Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/songlab/omim/test.parquet")
- Polars
import polars as pl
df = pl.read_parquet("https://huggingface.co/datasets/songlab/omim/resolve/main/test.parquet")
- Datasets
from datasets import load_dataset
dataset = load_dataset("songlab/omim", split="test")
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Size of downloaded dataset files:
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Size of the auto-converted Parquet files:
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Number of rows:
2,640,672