Variant report

Variant	rs16925055
Chromosome Location	chr9:108677437-108677438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108672824..108675555-chr9:108676544..108678880,2	MCF-7	breast:
2	chr9:108669187..108678029-chr9:108711816..108723206,29	MCF-7	breast:
3	chr9:108674312..108676473-chr9:108677250..108680180,2	K562	blood:
4	chr9:108677046..108679182-chr9:108680065..108682717,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12001361	0.95[AFR][1000 genomes]
rs12001396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12004099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13302213	0.82[EUR][1000 genomes]
rs16925065	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16925083	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17285222	0.82[EUR][1000 genomes]
rs1987249	0.95[AFR][1000 genomes]
rs34235964	0.85[EUR][1000 genomes]
rs34773238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35115335	1.00[EUR][1000 genomes]
rs56105641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788162	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59888664	0.82[AFR][1000 genomes]
rs60607803	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61312776	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7031020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71494570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71494574	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7847775	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7850106	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7861494	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16925055	DUSP4	trans	brain	seeQTL
rs16925055	FCER2	trans	brain	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108673000-108677800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr9:108673800-108679000	Enhancers	HMEC	breast
3	chr9:108674000-108677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:108674000-108683600	Weak transcription	Left Ventricle	heart
5	chr9:108674200-108677600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:108674400-108683000	Weak transcription	Fetal Heart	heart
7	chr9:108674600-108677600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr9:108674600-108683600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:108675200-108678200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:108675400-108680800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:108675800-108678200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:108676000-108677800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr9:108676000-108678200	Weak transcription	NHEK	skin
14	chr9:108676200-108678400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:108676400-108677600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:108676600-108677600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:108676600-108677600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:108676600-108682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:108676800-108679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:108677000-108680400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:108677400-108677600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr9:108677400-108680600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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