Variant report

Variant	rs558788
Chromosome Location	chr11:59852078-59852079
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	GATA3	chr11:59852014-59852936	T-47D	breast:	n/a	n/a
2	FOXA1	chr11:59852058-59852716	T-47D	breast:	n/a	n/a
3	GATA3	chr11:59852069-59852676	T-47D	breast:	n/a	n/a
4	CEBPB	chr11:59852045-59852314	K562	blood:	n/a	n/a
5	CEBPB	chr11:59852064-59852355	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
MS4A2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11230147	1.00[CHB][hapmap]
rs11230160	1.00[CHB][hapmap]
rs11230161	1.00[CHB][hapmap]
rs1125357	1.00[CHB][hapmap]
rs1151065	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151103	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151105	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11600716	1.00[CHB][hapmap]
rs11605427	1.00[CHB][hapmap]
rs12453	0.88[CHB][hapmap]
rs1286162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1286170	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs1286171	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1286289	0.81[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1296390	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17528859	1.00[CHB][hapmap]
rs17529983	1.00[CHB][hapmap]
rs17602572	0.88[CHB][hapmap]
rs2070970	1.00[CHB][hapmap]
rs2278867	0.88[CHB][hapmap]
rs2583471	1.00[CHB][hapmap]
rs2583476	1.00[CHB][hapmap]
rs2847663	1.00[CHB][hapmap]
rs2847668	1.00[CHB][hapmap]
rs2855017	1.00[CHB][hapmap]
rs3016834	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016835	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016836	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs471457	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939311	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs501697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501945	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs525828	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536531	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs539360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs543695	0.88[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs549651	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549680	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554311	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs558678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560238	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564912	0.89[CHB][hapmap]
rs579721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7121429	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7935829	0.88[CHB][hapmap]
rs920573	1.00[CHB][hapmap];0.81[CHD][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	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv972036	chr11:59845745-59853677	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59851800-59852800	Enhancers	Fetal Brain Male	brain
2	chr11:59852000-59853400	Enhancers	K562	blood

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