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Status
Public on Dec 01, 2012
Title
Whole blood 156
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: 2664
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
0.989
1.688
361
22916
0.029
1.658
0.9983
0.1506
rs1000002
NC
NC
0.978
0.788
328
10239
0.027
0.761
0.9976
-0.0728
rs10000023
AB
AC
0.474
2.240
11367
14865
1.167
1.074
0.5163
-0.0445
rs1000003
AA
AA
0.024
1.033
9431
586
0.995
0.038
0.0000
-0.3320
rs10000030
NC
NC
0.966
0.491
256
5945
0.025
0.466
0.9830
-0.2758
rs10000037
BB
GG
0.992
0.815
148
10256
0.010
0.805
1.0000
-0.1392
rs10000041
AA
AA
0.020
1.334
11168
589
1.293
0.041
0.0000
-0.3673
rs10000042
BB
GG
0.981
0.598
202
8025
0.017
0.580
1.0000
-0.5211
rs10000049
AA
AA
0.016
1.185
12794
501
1.156
0.029
0.0000
0.0087
rs1000007
AA
AA
0.012
1.213
10286
340
1.191
0.022
0.0000
-0.0601
rs10000073
AA
AA
0.022
1.034
11060
587
0.999
0.035
0.0049
-0.1099
rs10000081
AB
AG
0.530
0.859
3999
6224
0.409
0.449
0.5067
-0.3332
rs10000092
AA
AA
0.027
0.606
5651
361
0.581
0.025
0.0000
-0.3713
rs10000105
BB
GG
0.980
1.223
496
18005
0.037
1.186
1.0000
0.1475
rs10000119
BB
GG
0.988
1.288
293
17474
0.024
1.264
1.0000
0.0571
rs10000124
BB
CC
0.982
1.235
398
16581
0.035
1.200
0.9973
-0.1776
rs10000154
AA
AA
0.011
0.802
7657
218
0.788
0.014
0.0000
-0.0026
rs1000016
AA
AA
0.022
0.607
5075
294
0.586
0.021
0.0000
-0.2550
rs10000160
BB
GG
0.967
0.550
298
7231
0.027
0.523
0.9988
-0.5273
rs10000169
AB
AG
0.542
1.582
7204
11676
0.738
0.843
0.5052
0.2246
730525 46089 Kbytes .Supplementary data files not provided Processed data included within Sample table
