Variant report

Variant	rs2399685
Chromosome Location	chr11:93295334-93295335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93273580..93276539-chr11:93292460..93295434,2	K562	blood:

Variant related genes	Relation type
ENSG00000166002	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11020413	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11020415	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12416843	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12417178	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12791296	0.91[EUR][1000 genomes]
rs2399679	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2399680	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2399681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399682	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399683	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399684	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2895473	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4753086	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4753475	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753476	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4753477	0.93[EUR][1000 genomes]
rs60944979	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7118364	0.90[JPT][hapmap]
rs7125151	0.80[JPT][hapmap]
rs7126188	0.80[JPT][hapmap]
rs7939767	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2399685	PIWIL4	cis	parietal	SCAN
rs2399685	C11orf54	cis	parietal	SCAN
rs2399685	C11orf75	cis	lymphoblastoid	seeQTL
rs2399685	C11orf75	cis	multi-tissue	Pritchard
rs2399685	C11orf54	cis	cerebellum	SCAN
rs2399685	MED17	cis	parietal	SCAN
rs2399685	SCARNA9	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93294800-93295800	Enhancers	Rectal Mucosa Donor 29	rectum
2	chr11:93295200-93297400	Weak transcription	Fetal Intestine Large	intestine
3	chr11:93295200-93300200	Weak transcription	Liver	Liver

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