Variant report

Variant	rs11645898
Chromosome Location	chr16:72229532-72229533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72218659..72222633-chr16:72228772..72231216,3	K562	blood:
2	chr16:72229508..72230170-chr16:72241073..72241974,2	MCF-7	breast:
3	chr16:72227939..72230623-chr16:72263663..72265435,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11640722	1.00[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11641721	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11648479	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648622	0.96[GIH][hapmap]
rs17603936	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17604349	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs28419077	0.91[EUR][1000 genomes]
rs34656481	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34832584	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35370634	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35746112	0.89[EUR][1000 genomes]
rs3812985	0.96[GIH][hapmap];0.87[EUR][1000 genomes]
rs3852785	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4788459	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4788460	0.83[GIH][hapmap]
rs4788463	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788605	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4788611	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4788614	1.00[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs4788615	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55955726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7206422	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72787070	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72787077	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72787078	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72787085	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72787091	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72787093	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72787094	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72791112	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72791115	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72791117	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72791120	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72791121	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047881	0.86[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11645898	PMFBP1	cis	multi-tissue	Pritchard
rs11645898	HP	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72214800-72232800	Weak transcription	Pancreas	Pancrea
2	chr16:72222000-72235800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr16:72223000-72236400	Weak transcription	Primary B cells from cord blood	blood
4	chr16:72225800-72231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:72226000-72231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr16:72226000-72231400	Weak transcription	NHDF-Ad	bronchial
7	chr16:72228600-72231600	Enhancers	Fetal Brain Male	brain
8	chr16:72228600-72236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:72228800-72236600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:72229000-72229800	Enhancers	Fetal Brain Female	brain
11	chr16:72229000-72230600	Weak transcription	Brain Angular Gyrus	brain
12	chr16:72229200-72230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:72229200-72232800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:72229200-72234400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr16:72229200-72240200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:72229400-72229600	Weak transcription	Fetal Muscle Trunk	muscle

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