Variant report

Variant	rs1881316
Chromosome Location	chr16:31694063-31694064
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	chr16:31518111..31520799-chr16:31691550..31694170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140688	Chromatin interaction
ENSG00000260625	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1045483	0.82[CEU][hapmap]
rs10871458	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11150638	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1156903	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11642525	0.86[CEU][hapmap]
rs12324951	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12447780	0.83[ASN][1000 genomes]
rs12716999	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12717000	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12921028	0.82[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs1304163	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs1406177	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];1.00[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]
rs1406178	0.82[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap]
rs1468158	0.82[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap]
rs1468159	0.82[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap]
rs1528317	0.82[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs1528319	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1534507	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1599855	0.82[CEU][hapmap]
rs1852666	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1881318	0.82[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1919040	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1919042	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2091521	0.81[CEU][hapmap]
rs2106579	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2106581	1.00[ASN][1000 genomes]
rs2157970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2178179	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2222754	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2359222	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2359226	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2359455	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28427454	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2884713	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs3751738	0.82[CEU][hapmap]
rs3751742	0.82[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap]
rs4632148	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs4889553	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4889555	0.95[ASN][1000 genomes]
rs4889688	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4889693	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62054710	0.82[ASN][1000 genomes]
rs6565267	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6565269	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6565270	0.81[EUR][1000 genomes]
rs6565275	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6565278	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6565280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6565282	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6565285	0.82[JPT][hapmap]
rs6565286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6565287	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7188627	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7190730	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7197963	0.82[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap]
rs7198038	0.82[CEU][hapmap]
rs727349	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7359491	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs8048591	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs8048741	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs8049323	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8053712	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8060086	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8062424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8062902	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs916753	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs929208	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs929209	0.82[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs9921546	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9921898	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9928006	0.80[AMR][1000 genomes]
rs9929892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9930700	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9936002	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9938037	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][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	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	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv833195	chr16:31576112-31763222	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1057598	chr16:31608831-31726446	Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1881316	PRRT2	cis	parietal	SCAN
rs1881316	CD2BP2	cis	parietal	SCAN
rs1881316	TBX6	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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