Variant report

Variant	rs9936642
Chromosome Location	chr16:72209519-72209520
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	chr16:72205417..72207058-chr16:72209158..72210680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118557	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10400963	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852511	0.89[JPT][hapmap]
rs11075922	0.84[EUR][1000 genomes]
rs11075924	0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11643192	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12325266	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449073	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12928732	0.85[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12929749	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12932845	0.81[JPT][hapmap]
rs12935232	0.95[ASN][1000 genomes]
rs13334151	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs16973716	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs2070937	0.81[JPT][hapmap]
rs2241411	0.85[JPT][hapmap]
rs2288002	0.80[JPT][hapmap]
rs2550868	0.80[JPT][hapmap]
rs3764312	0.81[JPT][hapmap]
rs3812984	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3844425	0.90[JPT][hapmap]
rs3852782	0.90[JPT][hapmap]
rs3852784	0.90[JPT][hapmap]
rs3852788	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3902135	0.81[JPT][hapmap]
rs3909541	0.95[GIH][hapmap];0.95[JPT][hapmap]
rs3909543	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4238964	0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788609	0.90[JPT][hapmap]
rs4788610	0.90[JPT][hapmap]
rs6499562	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs7188058	0.81[JPT][hapmap]
rs7192848	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7198572	0.81[JPT][hapmap]
rs7201225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201643	0.81[JPT][hapmap]
rs7203426	0.80[JPT][hapmap]
rs7203821	0.81[JPT][hapmap]
rs7940	0.85[JPT][hapmap]
rs8044868	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes]
rs8052338	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8052408	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs8059437	0.85[JPT][hapmap]
rs9927526	0.85[JPT][hapmap]
rs9928157	0.85[JPT][hapmap]
rs9932951	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9936642	FAM65A	cis	cerebellum	SCAN
rs9936642	SLC12A4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72207000-72209800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:72208600-72209600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr16:72208800-72209600	Enhancers	Monocytes-CD14+_RO01746	blood

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