Variant report

Variant	rs11530830
Chromosome Location	chr11:58252992-58252993
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10792172	0.85[LWK][hapmap]
rs10896774	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10896775	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10896785	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896787	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10896788	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896794	0.84[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes]
rs10896795	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]
rs11229409	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs11229410	0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11229411	0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11229412	0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11229413	0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11229423	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11229463	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11229505	0.84[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11229512	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229519	0.84[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11229543	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11229545	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap]
rs11601687	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11605269	0.89[AMR][1000 genomes]
rs11605297	0.83[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11605683	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs12269745	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12274866	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12279895	0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12280114	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12285111	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12286421	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12289198	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12290089	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12291551	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12294062	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12786744	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12797488	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12800710	0.84[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12802819	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12802960	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12803648	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17474373	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17567523	0.89[AMR][1000 genomes]
rs1893902	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs1938637	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1986404	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2000486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2275993	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2298608	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap]
rs3168135	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap]
rs35279927	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4127353	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4323891	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4347409	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4506677	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4517537	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4519112	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4579945	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6591475	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7101864	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap]
rs7102510	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap]
rs7102852	0.89[AMR][1000 genomes]
rs7110210	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7925560	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7931394	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8373	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	67 gene(s)	inside rSNPs	diseases
2	nsv517849	chr11:58129053-58264181	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1042491	chr11:58134936-58263639	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv976518	chr11:58247628-58271109	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11530830	MS4A10	cis	cerebellum	SCAN
rs11530830	SERPING1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58252400-58265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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