Variant report

Variant	rs3923601
Chromosome Location	chr9:115911276-115911277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115887976..115889749-chr9:115910119..115911972,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10759626	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs10817450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10981648	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10981656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10981659	0.90[EUR][1000 genomes]
rs10981660	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1128150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs12340409	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs12350438	1.00[CHB][hapmap]
rs12352536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12378957	0.93[EUR][1000 genomes]
rs3923602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs3935395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs4273923	0.93[EUR][1000 genomes]
rs72756152	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7467882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831691	chr9:115754699-115929459	Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv893743	chr9:115867276-115917783	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1038107	chr9:115881588-115911276	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1051654	chr9:115881588-115935663	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv615212	chr9:115891009-115915859	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv466507	chr9:115905850-115936903	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv615213	chr9:115905850-115936903	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115899000-115913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:115900600-115913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:115902800-115912600	Weak transcription	Brain Angular Gyrus	brain
4	chr9:115903400-115912600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:115909200-115912000	Enhancers	Placenta	Placenta
6	chr9:115909600-115912600	Enhancers	Brain Hippocampus Middle	brain
7	chr9:115910000-115912400	Weak transcription	Brain Anterior Caudate	brain
8	chr9:115910000-115912400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:115910000-115912800	Enhancers	Liver	Liver
10	chr9:115910000-115912800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:115910600-115912800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:115911000-115911800	Weak transcription	Brain Substantia Nigra	brain
13	chr9:115911000-115912000	Enhancers	Spleen	Spleen
14	chr9:115911000-115912000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr9:115911000-115912800	Enhancers	HepG2	liver

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