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Status
Public on Dec 01, 2012
Title
Whole blood 146
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: 3603
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
BB
GG
0.994
1.612
234
18862
0.015
1.596
1.0000
0.0898
rs1000002
NC
NC
0.979
0.727
275
8140
0.023
0.704
0.9992
-0.1869
rs10000023
AB
AC
0.462
2.307
11044
12851
1.223
1.084
0.5049
-0.0109
rs1000003
AA
AA
0.032
1.046
8785
660
0.997
0.049
0.0000
-0.3158
rs10000030
NC
NC
0.835
0.435
749
3729
0.091
0.344
0.6221
-0.2927
rs10000037
AB
AG
0.490
1.035
4159
5546
0.526
0.510
0.5230
-0.0841
rs10000041
AA
AA
0.025
1.553
11715
736
1.493
0.060
0.0042
-0.1474
rs10000042
BB
GG
0.961
0.852
483
9499
0.049
0.803
0.9932
-0.0207
rs10000049
AA
AA
0.024
1.351
13216
765
1.301
0.049
0.0016
0.1935
rs1000007
AA
AA
0.007
1.330
10320
237
1.315
0.015
0.0000
0.0747
rs10000073
AA
AA
0.014
0.998
9909
378
0.975
0.022
0.0000
-0.1592
rs10000081
AB
AG
0.505
1.008
4516
6026
0.500
0.508
0.4811
-0.1002
rs10000092
AB
AG
0.533
0.774
3314
4822
0.367
0.407
0.5295
-0.1029
rs10000105
BB
GG
0.992
1.251
260
15955
0.016
1.236
1.0000
0.1874
rs10000119
BB
GG
0.987
1.292
299
14978
0.025
1.267
1.0000
0.0615
rs10000124
BB
CC
0.979
1.212
408
13874
0.038
1.174
0.9955
-0.2067
rs10000154
AA
AA
0.016
0.843
7376
277
0.822
0.020
0.0000
0.0668
rs1000016
AB
AG
0.538
0.589
2201
3398
0.277
0.312
0.4952
-0.3265
rs10000160
BB
GG
0.971
0.712
315
8046
0.031
0.680
1.0000
-0.1546
rs10000169
AA
AA
0.027
1.311
11297
674
1.258
0.053
0.0022
0.2006
730525 46007 Kbytes .Supplementary data files not provided Processed data included within Sample table
