Variant report

Variant	rs1104845
Chromosome Location	chr15:56112394-56112395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56111924..56113965-chr15:56117749..56120711,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1104848	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12899701	0.84[EUR][1000 genomes]
rs12906245	0.85[EUR][1000 genomes]
rs12906350	0.85[EUR][1000 genomes]
rs12907101	0.95[AMR][1000 genomes]
rs12908286	0.81[EUR][1000 genomes]
rs12908466	0.84[EUR][1000 genomes]
rs12911101	0.81[EUR][1000 genomes]
rs12913220	0.85[EUR][1000 genomes]
rs17819216	0.90[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[AMR][1000 genomes]
rs17819222	0.90[CEU][hapmap];0.95[AMR][1000 genomes]
rs17819228	0.90[CEU][hapmap];0.95[AMR][1000 genomes]
rs1912403	0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2899593	0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs34146683	1.00[AMR][1000 genomes]
rs34247233	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34333169	0.81[EUR][1000 genomes]
rs34685895	0.95[AMR][1000 genomes]
rs34755247	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35299498	0.95[AMR][1000 genomes]
rs35313340	0.81[EUR][1000 genomes]
rs35472570	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35734155	0.95[AMR][1000 genomes]
rs35759462	0.85[EUR][1000 genomes]
rs35941636	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36132540	0.86[AMR][1000 genomes]
rs7182185	0.81[CEU][hapmap];1.00[MKK][hapmap];0.95[AMR][1000 genomes]
rs72732242	1.00[AMR][1000 genomes]
rs8033157	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs906811	0.87[GIH][hapmap];0.91[TSI][hapmap]
rs933997	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1104845	TMOD3	cis	cerebellum	SCAN
rs1104845	CYP19A1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56095800-56128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56106000-56131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56111000-56115000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:56111000-56115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:56111000-56115200	Weak transcription	Osteobl	bone
6	chr15:56111200-56112600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:56111800-56112400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:56111800-56112400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:56111800-56112400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:56111800-56112800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr15:56112000-56112600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:56112000-56112600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:56112000-56112600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:56112000-56112600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:56112000-56113000	Enhancers	Brain Germinal Matrix	brain
16	chr15:56112200-56112400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:56112200-56112400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:56112200-56112600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:56112200-56121800	Weak transcription	Fetal Muscle Trunk	muscle

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