Variant report

Variant	rs9926110
Chromosome Location	chr16:71565582-71565583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71563743..71565886-chr16:71567362..71568965,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10500558	0.97[ASN][1000 genomes]
rs11640165	0.97[ASN][1000 genomes]
rs11641492	0.97[ASN][1000 genomes]
rs11643216	0.97[ASN][1000 genomes]
rs11644434	0.81[CHB][hapmap]
rs11647749	0.98[ASN][1000 genomes]
rs12446461	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12597011	1.00[YRI][hapmap]
rs12597949	1.00[YRI][hapmap]
rs13331346	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1609868	0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1609869	0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs16973266	0.82[CHB][hapmap]
rs172649	0.81[CHD][hapmap]
rs2004672	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070832	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2288486	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs2288487	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs2288488	0.92[ASN][1000 genomes]
rs2303788	0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs2432524	0.88[CHB][hapmap];0.83[GIH][hapmap]
rs28372238	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs310334	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35373081	0.89[ASN][1000 genomes]
rs35916432	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3813743	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3892120	0.83[AMR][1000 genomes]
rs4149497	1.00[YRI][hapmap]
rs4149498	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs4503795	0.91[ASN][1000 genomes]
rs4620964	0.91[CEU][hapmap];0.88[AMR][1000 genomes]
rs58134724	0.91[ASN][1000 genomes]
rs58452291	0.85[ASN][1000 genomes]
rs58719913	0.97[ASN][1000 genomes]
rs59819114	0.82[ASN][1000 genomes]
rs6499523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7184543	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs7186241	0.98[ASN][1000 genomes]
rs7187165	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs7187354	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188342	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs7192986	0.83[AMR][1000 genomes]
rs7199026	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs7199373	0.91[ASN][1000 genomes]
rs7200335	0.93[ASN][1000 genomes]
rs7200431	1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs7202662	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs7202953	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs730470	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs732318	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74026831	0.98[ASN][1000 genomes]
rs74027246	0.97[ASN][1000 genomes]
rs8044068	0.99[ASN][1000 genomes]
rs8044561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8051212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053662	0.97[ASN][1000 genomes]
rs8058294	1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs8058776	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8061078	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9302623	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9928243	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9933680	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs9935426	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9936249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9940771	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv906892	chr16:71526720-71570413	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9926110	DYNC1LI2	cis	cerebellum	SCAN
rs9926110	PHLPP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71560600-71583400	Weak transcription	Pancreas	Pancrea
2	chr16:71561000-71582400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:71561200-71576400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:71565200-71565600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:71565400-71565600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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