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Status
Public on Dec 01, 2012
Title
Whole blood 84
Sample type
genomic
Source name
Whole blood
Organism
Homo sapiens Characteristics
gender: F
Extracted molecule
genomic DNA
Extraction protocol
Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)
Label
Biotin-NTP
Label protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Hybridization protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Scan protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Description
sample id: 3786
Data processing
Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips
Submission date
Sep 30, 2012
Last update date
Dec 01, 2012
Contact name
Boyko Kabakchiev
Organization name
Mount Sinai Hospital
Department
Samuel Lunenfeld Research Institute
Lab
Silverberg Lab
Street address
60 Murray Street, Room L3-004
City
Toronto
State/province
Ontario
ZIP/Postal code
M5T 3L9
Country
Canada
Platform ID
GPL13135 Series (2)
GSE41238 eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Illumina SNP)
GSE41269 eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine
Data table header descriptions ID_REF VALUE SNP Calls
Top Geno HumanOmniExpress_12v1: Top Geno in NN format where N equals A, T, C, G, - ; HumanOmni2.5-Quad_4v1: Top Alleles in NN format where N equals A, T, C, G, -
Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio
Data table ID_REF VALUE Top Geno Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio rs1000000
AB
AG
0.388
2.251
13045
11882
1.325
0.926
0.4600
0.0534
rs1000002
NC
NC
0.405
0.987
5475
5300
0.568
0.420
0.4792
-0.0242
rs10000023
AA
AA
0.020
1.786
17016
719
1.732
0.054
0.0000
-0.1778
rs1000003
AA
AA
0.027
1.093
10063
596
1.049
0.044
0.0000
-0.2511
rs10000030
NC
NC
0.985
0.577
154
6599
0.013
0.564
1.0000
-0.0657
rs10000037
AB
AG
0.494
1.141
4904
6623
0.576
0.565
0.5265
0.0583
rs10000041
AB
AC
0.429
1.409
6653
7341
0.783
0.626
0.5387
-0.2051
rs10000042
BB
GG
0.979
0.930
340
11523
0.030
0.899
1.0000
0.1148
rs10000049
AA
AA
0.019
1.185
12594
514
1.151
0.034
0.0000
0.0067
rs1000007
AA
AA
0.010
1.286
10698
275
1.266
0.021
0.0000
0.0254
rs10000073
AB
AG
0.567
1.170
5772
8949
0.523
0.647
0.5049
-0.1023
rs10000081
AB
AG
0.536
0.979
4560
6638
0.461
0.517
0.5140
-0.1410
rs10000092
AA
AA
0.012
0.788
7604
213
0.773
0.015
0.0000
0.0108
rs10000105
BB
GG
0.978
1.226
532
16349
0.040
1.186
1.0000
0.1500
rs10000119
BB
GG
0.985
1.237
336
15470
0.029
1.208
1.0000
-0.0036
rs10000124
BB
CC
0.985
1.230
327
15397
0.028
1.202
1.0000
-0.1795
rs10000154
BB
GG
0.979
0.867
313
10752
0.028
0.839
1.0000
0.0874
rs1000016
AB
AG
0.570
0.726
2762
4730
0.323
0.403
0.5313
-0.0185
rs10000160
BB
GG
0.979
0.729
262
9054
0.023
0.706
1.0000
-0.1156
rs10000169
AB
AG
0.518
1.452
6956
9579
0.705
0.747
0.4812
0.1074
730525 46042 Kbytes .Supplementary data files not provided Processed data included within Sample table
