Variant report

Variant	rs17159904
Chromosome Location	chr11:85786287-85786288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85785404..85787947-chr11:85789787..85792385,3	K562	blood:
2	chr11:85779081..85782313-chr11:85782461..85788148,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10128700	0.83[EUR][1000 genomes]
rs10501603	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs10501605	0.81[EUR][1000 genomes]
rs10501607	0.81[EUR][1000 genomes]
rs10898431	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11234517	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs11234544	0.89[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs11234548	0.81[EUR][1000 genomes]
rs12270433	0.83[EUR][1000 genomes]
rs12271390	0.81[EUR][1000 genomes]
rs12276435	0.81[EUR][1000 genomes]
rs12277986	0.81[EUR][1000 genomes]
rs12281494	0.90[EUR][1000 genomes]
rs12282655	0.88[EUR][1000 genomes]
rs12284629	0.83[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs12294130	0.83[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs17745236	0.80[EUR][1000 genomes]
rs17745248	0.83[EUR][1000 genomes]
rs17745273	0.86[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17817859	0.81[EUR][1000 genomes]
rs17817883	0.81[EUR][1000 genomes]
rs17817919	0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs17817956	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2001241	0.88[EUR][1000 genomes]
rs4943934	0.81[EUR][1000 genomes]
rs4943937	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs4944550	0.88[CEU][hapmap]
rs4944554	0.80[EUR][1000 genomes]
rs4944555	0.84[EUR][1000 genomes]
rs4944556	0.83[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55791429	0.85[EUR][1000 genomes]
rs55815523	0.82[EUR][1000 genomes]
rs56026701	0.80[EUR][1000 genomes]
rs56187740	0.85[EUR][1000 genomes]
rs56207019	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58937798	0.80[EUR][1000 genomes]
rs7128598	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72950443	0.88[EUR][1000 genomes]
rs72950453	0.88[EUR][1000 genomes]
rs72950456	0.88[EUR][1000 genomes]
rs72959906	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72959929	0.81[EUR][1000 genomes]
rs72961110	0.80[EUR][1000 genomes]
rs72963086	0.80[EUR][1000 genomes]
rs72963092	0.81[EUR][1000 genomes]
rs72965157	0.83[EUR][1000 genomes]
rs72965166	0.88[EUR][1000 genomes]
rs7927222	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs7943152	0.83[CEU][hapmap];0.90[EUR][1000 genomes]

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	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17159904	PICALM	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85781400-85796000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:85785600-85788600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:85785800-85788400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:85785800-85789800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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