Variant report

Variant	rs10853547
Chromosome Location	chr18:44530548-44530549
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44529742..44530665-chr18:44562546..44563169,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10070	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10853544	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10853545	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11082562	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660085	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12386118	0.93[ASN][1000 genomes]
rs1465722	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1539878	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];0.99[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789152	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1893427	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1970668	0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2010834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2032215	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2051292	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2156050	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2187090	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2187091	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2187092	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571024	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2571026	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2571028	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs2576040	0.82[GIH][hapmap]
rs2576042	0.82[GIH][hapmap]
rs2576050	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2576051	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744863	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3892820	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4258717	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs477826	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4890341	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4890342	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4890343	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4890347	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4890698	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs4890699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890700	0.93[ASN][1000 genomes]
rs4890703	0.91[EUR][1000 genomes]
rs4890707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs501062	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs501882	0.88[JPT][hapmap]
rs504668	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs513775	0.92[CHD][hapmap];0.98[GIH][hapmap]
rs530205	1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs553456	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs577200	0.89[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs578451	0.88[JPT][hapmap]
rs590923	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs593340	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs605487	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs607780	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs616900	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs626217	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs641366	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs642897	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs644731	0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs646128	1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs649076	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6507709	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs6507714	0.91[EUR][1000 genomes]
rs658756	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs680018	0.88[JPT][hapmap]
rs695001	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7227700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7234570	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7240239	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7244013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7245049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8086286	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs8089938	0.83[EUR][1000 genomes]
rs8091984	0.83[AMR][1000 genomes]
rs8094654	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8095373	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];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096263	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8097455	0.81[CEU][hapmap]
rs892586	0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs9304336	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs9304337	0.89[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs9304338	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304339	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9304340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945443	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9947131	0.96[ASN][1000 genomes]
rs9948405	0.81[ASN][1000 genomes]
rs9954336	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs9959877	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9960463	0.81[AMR][1000 genomes]
rs9962523	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9966646	0.95[ASN][1000 genomes]
rs998819	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833639	chr18:44426363-44552719	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv576813	chr18:44481641-44531283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1057629	chr18:44500259-44539223	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1062444	chr18:44503472-44539223	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1062682	chr18:44509052-44539223	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1056744	chr18:44509052-44581752	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv909609	chr18:44513071-44597092	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv1818108	chr18:44519357-44549177	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1825684	chr18:44526351-44549177	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10853547	PIAS2	cis	multi-tissue	Pritchard
rs10853547	ST8SIA5	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44527400-44531200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:44527400-44538800	Weak transcription	Brain Hippocampus Middle	brain

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