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Status
Public on Dec 01, 2012
Title
Whole blood 53
Sample type
genomic
Source name
Whole blood
Organism
Homo sapiens Characteristics
gender: M
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: 4043
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
0.985
1.480
648
23839
0.034
1.446
0.9952
-0.0427
rs1000002
NC
NC
0.404
1.000
7410
6984
0.576
0.424
0.4781
-0.0057
rs10000023
AA
AA
0.022
1.772
22341
1213
1.712
0.060
0.0011
-0.1904
rs1000003
AA
AA
0.025
0.985
12056
798
0.948
0.038
0.0000
-0.4011
rs10000030
NC
NC
0.781
0.553
1742
6230
0.146
0.407
0.4915
0.1179
rs10000037
BB
GG
0.972
0.885
571
12948
0.038
0.847
1.0000
-0.0338
rs10000041
AA
AA
0.026
1.407
15592
1080
1.351
0.056
0.0051
-0.2897
rs10000042
BB
GG
0.971
0.905
641
14268
0.040
0.865
1.0000
0.0717
rs10000049
AA
AA
0.032
1.422
19555
1443
1.354
0.068
0.0094
0.2647
rs1000007
AA
AA
0.008
1.281
14592
445
1.265
0.015
0.0000
0.0200
rs10000073
AA
AA
0.018
0.985
13841
649
0.958
0.027
0.0009
-0.1794
rs10000081
AA
AA
0.046
0.840
10229
1039
0.784
0.057
0.0115
-0.2461
rs10000092
AB
AG
0.483
0.930
6286
7525
0.477
0.453
0.4768
0.1570
rs10000105
BB
GG
0.987
1.205
541
20947
0.024
1.181
1.0000
0.1297
rs10000119
BB
GG
0.983
1.332
644
21371
0.035
1.297
1.0000
0.1022
rs10000124
BB
CC
0.981
1.202
617
19239
0.035
1.167
0.9970
-0.2170
rs10000154
AB
AG
0.514
1.011
6521
8584
0.494
0.517
0.4619
0.2015
rs1000016
AA
AA
0.045
0.657
7064
758
0.613
0.044
0.0174
-0.1430
rs10000160
BB
GG
0.953
0.754
778
11569
0.052
0.701
0.9813
-0.0791
rs10000169
AB
AG
0.530
1.513
9527
13143
0.721
0.792
0.4922
0.1624
730525 46299 Kbytes .Supplementary data files not provided Processed data included within Sample table
