Variant report

Variant	rs17269903
Chromosome Location	chr11:34512109-34512110
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	chr11:34508412..34512527-chr11:34512601..34514689,3	MCF-7	breast:
2	chr11:34508032..34510036-chr11:34510118..34513690,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1008491	0.92[ASN][1000 genomes]
rs10836230	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10836234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11032661	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11032667	0.81[ASN][1000 genomes]
rs11032669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11032670	0.81[ASN][1000 genomes]
rs11032671	0.81[ASN][1000 genomes]
rs11032682	0.89[ASN][1000 genomes]
rs11032695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11032718	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032722	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032723	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032724	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032728	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12361866	0.81[ASN][1000 genomes]
rs12790004	0.81[ASN][1000 genomes]
rs12790145	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12790378	0.81[ASN][1000 genomes]
rs12793666	0.89[ASN][1000 genomes]
rs12797675	0.96[CEU][hapmap]
rs12804506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12804689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12806377	0.81[ASN][1000 genomes]
rs12807961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12808450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1408041	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535719	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17269931	0.96[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17352313	0.81[ASN][1000 genomes]
rs2146962	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231825	0.96[CEU][hapmap]
rs2231828	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2420386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34329347	0.89[ASN][1000 genomes]
rs34366473	0.86[EUR][1000 genomes]
rs34533645	0.89[ASN][1000 genomes]
rs34901344	0.86[EUR][1000 genomes]
rs35725681	0.89[ASN][1000 genomes]
rs475043	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs494024	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs499406	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs508370	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs511895	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs524167	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533425	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55898107	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs560807	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59090359	0.81[ASN][1000 genomes]
rs66679411	0.89[ASN][1000 genomes]
rs737254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873466	0.81[ASN][1000 genomes]
rs910089	0.81[ASN][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	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17269903	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs17269903	CAT	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34511600-34512400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:34511600-34512800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:34511800-34512200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:34512000-34512800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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