Variant report

Variant	rs16925032
Chromosome Location	chr9:108662938-108662939
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108662761..108665200-chr9:108718437..108720079,2	MCF-7	breast:
2	chr9:108660253..108666422-chr9:108715149..108718235,9	MCF-7	breast:
3	chr9:108662735..108665889-chr9:109622755..109626966,6	MCF-7	breast:
4	chr9:108658836..108662386-chr9:108662597..108665085,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148143	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10115085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10117602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10120538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739215	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759148	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759149	0.81[EUR][1000 genomes]
rs10759150	0.81[EUR][1000 genomes]
rs10759151	0.81[EUR][1000 genomes]
rs10759152	0.81[EUR][1000 genomes]
rs10816352	1.00[ASN][1000 genomes]
rs10978330	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978331	1.00[ASN][1000 genomes]
rs10978332	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978340	0.82[EUR][1000 genomes]
rs13296649	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1987136	0.81[EUR][1000 genomes]
rs2417643	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417644	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417650	0.95[ASN][1000 genomes]
rs2417656	0.97[ASN][1000 genomes]
rs2900404	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4598317	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742658	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742967	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742969	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742972	0.83[AMR][1000 genomes]
rs4742974	0.80[EUR][1000 genomes]
rs6477482	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043384	0.80[EUR][1000 genomes]
rs7044156	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7856876	0.81[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

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108662600-108664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:108662800-108663000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:108662800-108664200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:108662800-108664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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