Variant report

Variant	rs543695
Chromosome Location	chr11:59845829-59845830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1151065	0.83[EUR][1000 genomes]
rs1151103	0.83[EUR][1000 genomes]
rs1151104	0.87[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs1151105	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286162	0.85[EUR][1000 genomes]
rs1286169	0.88[CEU][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1286170	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1286171	0.82[EUR][1000 genomes]
rs1286289	0.93[GIH][hapmap];0.83[MEX][hapmap]
rs1296390	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3016834	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3016835	0.84[AMR][1000 genomes]
rs471457	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs474951	0.88[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501697	0.88[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501945	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs525828	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs528823	0.88[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs536531	0.83[EUR][1000 genomes]
rs539360	0.88[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs549651	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs549680	0.84[EUR][1000 genomes]
rs554311	0.83[EUR][1000 genomes]
rs558678	0.88[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs558788	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]
rs579721	0.88[CEU][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]

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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs543695	SCGB2A2	cis	cerebellum	SCAN
rs543695	MPEG1	cis	lymphoblastoid	seeQTL
rs543695	MS4A4A	cis	multi-tissue	Pritchard
rs543695	C11orf9	cis	parietal	SCAN
rs543695	SYT7	cis	parietal	SCAN
rs543695	POLR2G	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59844000-59847600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:59844800-59846400	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr11:59845400-59846000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr11:59845600-59846600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:59845800-59846600	Enhancers	K562	blood

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