Variant report

Variant	rs1286289
Chromosome Location	chr11:59826677-59826678
allele	A/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	FOS	chr11:59826529-59826883	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
2	EGR1	chr11:59826532-59826855	K562	blood:	n/a	n/a
3	FOS	chr11:59826552-59826883	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
4	FOS	chr11:59826542-59826896	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
5	BATF	chr11:59826600-59826779	GM12878	blood:	n/a	chr11:59826708-59826719
6	BATF	chr11:59826577-59826779	GM12878	blood:	n/a	chr11:59826708-59826719
7	FOSL1	chr11:59826599-59826815	K562	blood:	n/a	chr11:59826710-59826721
8	FOS	chr11:59826551-59826855	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
9	EP300	chr11:59826614-59826804	K562	blood:	n/a	n/a
10	FOS	chr11:59826660-59826835	HUVEC	blood vessel:	n/a	chr11:59826710-59826721
11	EGR1	chr11:59826595-59826860	K562	blood:	n/a	n/a
12	EP300	chr11:59826622-59826830	GM12878	blood:	n/a	n/a
13	ATF3	chr11:59826579-59826826	K562	blood:	n/a	n/a
14	JUN	chr11:59826580-59826850	K562	blood:	n/a	n/a
15	JUND	chr11:59826542-59826927	K562	blood:	n/a	chr11:59826710-59826721
16	JUND	chr11:59826608-59826852	HepG2	liver:	n/a	chr11:59826710-59826721
17	JUN	chr11:59826001-59827014	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59822049..59824288-chr11:59826581..59828945,2	K562	blood:

Variant related genes	Relation type
MS4A3	TF binding region
ENSG00000149516	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1151065	0.88[EUR][1000 genomes]
rs1151102	0.83[CHB][hapmap]
rs1151103	0.88[EUR][1000 genomes]
rs1151104	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs1286162	0.86[EUR][1000 genomes]
rs1286169	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1286170	0.80[CEU][hapmap]
rs1286171	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1296390	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3016834	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3016835	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3016836	0.83[EUR][1000 genomes]
rs471457	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs474951	0.81[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs501697	0.81[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs501945	0.86[EUR][1000 genomes]
rs525828	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs528823	0.81[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs536531	0.88[EUR][1000 genomes]
rs539360	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs543695	0.93[GIH][hapmap];0.83[MEX][hapmap]
rs549651	0.86[EUR][1000 genomes]
rs549680	0.85[EUR][1000 genomes]
rs554311	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs558678	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs558788	0.81[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs579721	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs663925	0.83[CHB][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1286289	ZBTB3	cis	cerebellum	SCAN
rs1286289	SCGB2A2	cis	cerebellum	SCAN
rs1286289	SYT7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59822800-59832000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:59824600-59830000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59825000-59827000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr11:59826400-59828400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:59826600-59829600	Weak transcription	K562	blood

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