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Status
Public on Dec 01, 2012
Title
Whole blood 90
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: 2786
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
0.990
1.437
182
10281
0.022
1.415
0.9994
-0.0794
rs1000002
NC
NC
0.384
0.952
3881
2794
0.564
0.389
0.4525
-0.0782
rs10000023
AA
AA
0.012
1.696
11624
270
1.664
0.032
0.0000
-0.2485
rs1000003
AB
AG
0.504
1.106
3789
3992
0.549
0.556
0.5499
-0.2919
rs10000030
NC
NC
0.982
0.590
128
3900
0.017
0.574
1.0000
-0.0284
rs10000037
BB
GG
0.971
0.864
262
5619
0.037
0.827
1.0000
-0.0686
rs10000041
AA
AA
0.026
1.509
9017
439
1.450
0.060
0.0051
-0.1885
rs10000042
BB
GG
0.989
0.897
135
6403
0.016
0.882
1.0000
0.0699
rs10000049
AB
AC
0.515
1.242
4769
5014
0.607
0.636
0.4939
-0.1342
rs1000007
AA
AA
0.015
1.328
8072
239
1.298
0.031
0.0013
0.0702
rs10000073
AA
AA
0.014
1.056
8091
220
1.034
0.022
0.0000
-0.0765
rs10000081
AA
AA
0.031
0.825
5509
293
0.787
0.038
0.0000
-0.2688
rs10000092
AA
AA
0.015
0.814
5565
156
0.795
0.019
0.0000
0.0571
rs10000105
BB
GG
0.983
1.289
313
9847
0.034
1.255
1.0000
0.2254
rs10000119
BB
GG
0.981
1.293
283
9123
0.037
1.256
1.0000
0.0585
rs10000124
BB
CC
0.988
1.214
187
8651
0.023
1.191
1.0000
-0.1960
rs10000154
AA
AA
0.021
0.859
5821
215
0.832
0.027
0.0000
0.0933
rs1000016
AA
AA
0.019
0.579
3505
129
0.562
0.017
0.0000
-0.3233
rs10000160
BB
GG
0.947
0.832
474
5576
0.064
0.768
0.9740
0.0612
rs10000169
AA
AA
0.014
1.366
9342
246
1.337
0.030
0.0000
0.2668
730525 45698 Kbytes .Supplementary data files not provided Processed data included within Sample table
