Variant report

Variant	rs12926250
Chromosome Location	chr16:72213316-72213317
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr16:72212874-72213886	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr16:72212954-72213468	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr16:72212975-72213491	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72125540..72128099-chr16:72212951..72214515,2	MCF-7	breast:

Variant related genes	Relation type
PMFBP1	TF binding region
ENSG00000140830	Chromatin interaction
ENSG00000140829	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11554764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12920842	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12923749	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925943	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12926119	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12927014	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12928056	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12933376	0.83[EUR][1000 genomes]
rs12933482	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12934523	0.83[EUR][1000 genomes]
rs17588429	1.00[CHB][hapmap]
rs17590101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17603662	1.00[JPT][hapmap]
rs17604662	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604676	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17666271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17667639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17667675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs34139543	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34682685	0.82[AMR][1000 genomes]
rs35079155	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35448862	0.89[ASN][1000 genomes]
rs35930480	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36012445	0.92[ASN][1000 genomes]
rs36061252	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36125653	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3815192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4788606	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4788612	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55772151	0.89[ASN][1000 genomes]
rs56901884	0.81[ASN][1000 genomes]
rs59049640	0.82[ASN][1000 genomes]
rs60449783	0.81[ASN][1000 genomes]
rs61060922	0.89[ASN][1000 genomes]
rs61258384	0.81[ASN][1000 genomes]
rs61404039	0.81[ASN][1000 genomes]
rs71386950	0.89[ASN][1000 genomes]
rs71386951	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7184117	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7191673	1.00[YRI][hapmap]
rs74029810	0.81[ASN][1000 genomes]
rs74029814	0.81[ASN][1000 genomes]
rs74029815	0.81[ASN][1000 genomes]
rs74029840	0.89[ASN][1000 genomes]
rs8057016	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8058214	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8061140	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8182209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9652628	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72213000-72213400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:72213000-72213600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr16:72213000-72213600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr16:72213000-72213800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr16:72213000-72213800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr16:72213000-72214000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:72213000-72214200	Enhancers	Duodenum Mucosa	Duodenum
8	chr16:72213000-72214400	Enhancers	Fetal Muscle Leg	muscle
9	chr16:72213200-72213800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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