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Status
Public on Dec 01, 2012
Title
Whole blood 49
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 HumanOmni Express and HumanOmni2.5-Quad Beadchips
Hybridization protocol
Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips
Scan protocol
Standard Illumina protocol for HumanOmni Express and Human
Description
sample id: 3922
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
0.986
1.405
358
15336
0.030
1.375
0.9960
-0.1167
rs1000002
NC
NC
0.979
0.842
342
8932
0.027
0.815
0.9988
0.0241
rs10000023
AB
AC
0.468
2.245
12086
11915
1.179
1.067
0.5112
-0.0451
rs1000003
AB
AG
0.526
0.933
4526
5346
0.447
0.486
0.5707
-0.5220
rs10000030
NC
NC
0.986
0.599
170
6062
0.013
0.585
1.0000
-0.0125
rs10000037
BB
GG
0.964
0.924
504
9047
0.050
0.874
0.9936
0.0239
rs10000041
BB
CC
0.981
0.949
311
9529
0.028
0.921
1.0000
-0.2737
rs10000042
BB
GG
0.976
0.893
372
9603
0.032
0.861
1.0000
0.0555
rs10000049
AA
AA
0.027
1.250
13600
663
1.198
0.051
0.0047
0.0801
rs1000007
AA
AA
0.010
1.244
11038
229
1.226
0.018
0.0000
-0.0224
rs10000073
AA
AA
0.018
0.953
10530
356
0.927
0.026
0.0011
-0.2262
rs10000081
AA
AA
0.037
0.809
7835
519
0.765
0.045
0.0026
-0.2982
rs10000092
BB
GG
0.987
0.755
197
8253
0.015
0.740
1.0000
0.0384
rs10000105
BB
GG
0.986
1.240
365
14497
0.026
1.214
1.0000
0.1706
rs10000119
BB
GG
0.985
1.239
331
13513
0.028
1.212
1.0000
-0.0002
rs10000124
BB
CC
0.991
1.203
220
13225
0.017
1.186
1.0000
-0.2064
rs10000154
AB
AG
0.520
0.960
4779
5533
0.465
0.495
0.4676
0.1243
rs1000016
AA
AA
0.031
0.595
5130
314
0.567
0.028
0.0035
-0.2844
rs10000160
BB
GG
0.974
0.680
308
7290
0.027
0.653
1.0000
-0.2193
rs10000169
AB
AG
0.567
1.586
7288
9786
0.709
0.876
0.5324
0.2396
730525 45993 Kbytes .Supplementary data files not provided Processed data included within Sample table
