Variant report

Variant	rs6591475
Chromosome Location	chr11:58193551-58193552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:58193467-58193602	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
OR5B2	TF binding region

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10750894	0.83[ASN][1000 genomes]
rs10750895	0.93[ASN][1000 genomes]
rs10750898	0.95[ASN][1000 genomes]
rs10792159	0.84[ASN][1000 genomes]
rs10792165	0.95[ASN][1000 genomes]
rs10896736	0.84[ASN][1000 genomes]
rs10896738	0.84[ASN][1000 genomes]
rs10896742	0.84[ASN][1000 genomes]
rs10896748	0.83[ASN][1000 genomes]
rs10896749	0.93[ASN][1000 genomes]
rs10896754	0.85[ASN][1000 genomes]
rs10896755	0.95[ASN][1000 genomes]
rs10896760	0.95[ASN][1000 genomes]
rs10896761	0.95[ASN][1000 genomes]
rs10896774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896775	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896785	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896787	0.85[AMR][1000 genomes]
rs10896788	0.85[AMR][1000 genomes]
rs10896794	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs10896795	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229304	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11229305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11229333	0.82[ASN][1000 genomes]
rs11229349	0.80[ASN][1000 genomes]
rs11229352	0.83[ASN][1000 genomes]
rs11229353	0.93[ASN][1000 genomes]
rs11229355	0.93[ASN][1000 genomes]
rs11229365	0.93[ASN][1000 genomes]
rs11229366	0.93[ASN][1000 genomes]
rs11229396	0.97[ASN][1000 genomes]
rs11229397	0.97[ASN][1000 genomes]
rs11229409	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11229410	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs11229411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs11229412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs11229413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs11229423	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11229505	0.83[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs11229512	0.87[AMR][1000 genomes]
rs11229519	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs11229543	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229545	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11530830	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11601687	0.87[AMR][1000 genomes]
rs11605269	0.87[AMR][1000 genomes]
rs11605297	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs11605683	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs11607488	0.97[ASN][1000 genomes]
rs12269745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12274866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12278357	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12279895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs12280114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12285111	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12289198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12290089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12291551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12294062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12575804	0.97[ASN][1000 genomes]
rs12786744	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12788786	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12789701	0.97[ASN][1000 genomes]
rs12797488	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12798255	0.97[ASN][1000 genomes]
rs12800710	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs12802819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12802960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803648	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12804134	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17474373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567523	0.87[AMR][1000 genomes]
rs1893902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1938637	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.95[ASN][1000 genomes]
rs1938646	0.93[ASN][1000 genomes]
rs1938647	0.93[ASN][1000 genomes]
rs1938662	0.93[ASN][1000 genomes]
rs1938663	0.93[ASN][1000 genomes]
rs1938664	0.93[ASN][1000 genomes]
rs1986404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000486	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2003231	0.97[ASN][1000 genomes]
rs2186407	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2226414	0.90[ASN][1000 genomes]
rs2275993	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs3168135	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs35279927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542119	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3887001	0.93[ASN][1000 genomes]
rs4085405	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4127345	0.82[ASN][1000 genomes]
rs4127346	0.84[ASN][1000 genomes]
rs4127348	0.93[ASN][1000 genomes]
rs4127353	0.86[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4288769	0.84[ASN][1000 genomes]
rs4323891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4347409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4439529	0.84[ASN][1000 genomes]
rs4439530	0.94[ASN][1000 genomes]
rs4506677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519112	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4544018	0.94[ASN][1000 genomes]
rs4561231	0.95[ASN][1000 genomes]
rs4579945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611223	0.90[ASN][1000 genomes]
rs4611224	0.93[ASN][1000 genomes]
rs4938893	0.83[ASN][1000 genomes]
rs6591469	0.93[ASN][1000 genomes]
rs7101864	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7102222	0.93[ASN][1000 genomes]
rs7102510	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7102784	0.84[ASN][1000 genomes]
rs7102852	0.87[AMR][1000 genomes]
rs7104814	0.82[ASN][1000 genomes]
rs7110210	0.87[AMR][1000 genomes]
rs7110266	0.93[ASN][1000 genomes]
rs7112318	0.86[ASN][1000 genomes]
rs7112578	0.87[ASN][1000 genomes]
rs7117244	0.93[ASN][1000 genomes]
rs7127035	0.84[ASN][1000 genomes]
rs734776	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs754681	0.95[ASN][1000 genomes]
rs7925560	0.87[AMR][1000 genomes]
rs7926741	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7930778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7931394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8373	0.84[CHB][hapmap];1.00[JPT][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6591475	MS4A10	cis	cerebellum	SCAN
rs6591475	SERPING1	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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