Variant report

Variant	rs580064
Chromosome Location	chr11:59869119-59869120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs107903	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1303615	0.89[CEU][hapmap]
rs1303621	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1441586	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1786137	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2847667	0.85[CEU][hapmap]
rs476722	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs483629	0.81[EUR][1000 genomes]
rs487997	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs502419	0.89[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs502581	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs504272	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs510518	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs512495	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs514266	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs516478	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs521952	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs525794	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs534273	0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs540170	1.00[ASW][hapmap];0.89[CEU][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs555635	0.89[CEU][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs556917	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs563803	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs564912	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs569046	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs574695	1.00[ASW][hapmap];0.89[CEU][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs574704	0.88[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs574798	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs580817	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs581133	0.82[ASW][hapmap];0.89[CEU][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs583296	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[LWK][hapmap];0.90[YRI][hapmap]
rs583791	0.82[CEU][hapmap]
rs595481	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs602396	0.89[CEU][hapmap]
rs606588	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs610932	0.82[CEU][hapmap]
rs617916	0.88[CEU][hapmap]
rs624663	0.81[CEU][hapmap]
rs631853	0.82[CEU][hapmap]
rs632185	0.82[CEU][hapmap]
rs652354	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs662196	0.82[CEU][hapmap]
rs684961	0.88[CEU][hapmap]
rs688030	0.88[CEU][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs580064	POLR2G	cis	cerebellum	SCAN
rs580064	FAM111A	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59865400-59870200	Enhancers	HUVEC	blood vessel
2	chr11:59866400-59875200	Weak transcription	Stomach Mucosa	stomach
3	chr11:59868000-59869400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:59868600-59869600	Weak transcription	Small Intestine	intestine
5	chr11:59868800-59869400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:59869000-59869400	Active TSS	Duodenum Mucosa	Duodenum

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