Variant report

Variant	rs12447780
Chromosome Location	chr16:31860399-31860400
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	chr16:31856392..31858498-chr16:31858989..31861220,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10871458	0.83[ASN][1000 genomes]
rs11150638	0.83[ASN][1000 genomes]
rs1156903	0.81[ASN][1000 genomes]
rs11644104	1.00[CEU][hapmap]
rs12716999	0.83[ASN][1000 genomes]
rs12717000	0.83[ASN][1000 genomes]
rs1406177	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs1528319	0.83[ASN][1000 genomes]
rs1881316	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs1919042	0.83[ASN][1000 genomes]
rs2106579	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2106581	0.83[ASN][1000 genomes]
rs2157970	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2359222	0.81[ASN][1000 genomes]
rs2359226	0.85[ASN][1000 genomes]
rs2359455	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs28427454	0.83[ASN][1000 genomes]
rs2884713	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs4889553	0.84[ASN][1000 genomes]
rs4889555	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4889688	0.83[ASN][1000 genomes]
rs4889693	0.88[ASN][1000 genomes]
rs6565269	0.81[ASN][1000 genomes]
rs6565278	0.85[ASN][1000 genomes]
rs6565280	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6565282	0.83[ASN][1000 genomes]
rs6565285	1.00[CEU][hapmap]
rs6565286	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6565287	0.85[ASN][1000 genomes]
rs7188627	0.85[ASN][1000 genomes]
rs7190730	0.85[ASN][1000 genomes]
rs727349	0.84[ASN][1000 genomes]
rs8048591	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs8049323	0.83[ASN][1000 genomes]
rs8053712	0.81[ASN][1000 genomes]
rs8060086	0.85[ASN][1000 genomes]
rs8062424	0.82[ASN][1000 genomes]
rs8062902	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs916753	0.85[ASN][1000 genomes]
rs929208	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs9921898	0.84[ASN][1000 genomes]
rs9928006	0.89[CEU][hapmap];0.80[MEX][hapmap]
rs9929892	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9930700	0.83[ASN][1000 genomes]
rs9936002	0.85[ASN][1000 genomes]
rs9938037	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[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	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3446880	chr16:31734687-31891223	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1066522	chr16:31831196-31959992	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12447780	STX1B	cis	cerebellum	SCAN
rs12447780	CD2BP2	cis	parietal	SCAN
rs12447780	PRR14	cis	parietal	SCAN
rs12447780	TBX6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31860000-31861200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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