Variant report

Variant	rs11227261
Chromosome Location	chr11:65462843-65462844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65461869..65464366-chr11:65623666..65626207,3	MCF-7	breast:
2	chr11:65429766..65432533-chr11:65462094..65464981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000173039	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10896027	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10896043	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11227248	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11227249	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11227250	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227283	0.83[ASN][1000 genomes]
rs11227284	0.80[ASN][1000 genomes]
rs11227288	0.80[ASN][1000 genomes]
rs11227302	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs1151488	0.85[CHB][hapmap]
rs1193851	0.85[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1205259	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12281400	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1784223	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1787034	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2448490	0.83[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2509948	0.87[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs3372	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs34007146	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34462081	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4930156	0.87[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4930304	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs494003	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs535111	0.82[YRI][hapmap]
rs573589	0.86[MEX][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs578056	0.80[ASN][1000 genomes]
rs7122657	0.85[CHB][hapmap]
rs7395672	0.82[MEX][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs7944860	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
2	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
3	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
6	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11227261	ZBTB3	cis	parietal	SCAN
rs11227261	RNASEH2C	cis	parietal	SCAN
rs11227261	AYP1p1	trans	multi-tissue	Pritchard
rs11227261	SIPA1	cis	cerebellum	SCAN
rs11227261	SNX32	cis	cerebellum	SCAN
rs11227261	RNASEH2C	cis	Artery Tibial	GTEx
rs11227261	SLC22A10	cis	parietal	SCAN
rs11227261	SNX32	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65459400-65466200	Enhancers	Stomach Mucosa	stomach
2	chr11:65460400-65463000	Weak transcription	Colonic Mucosa	Colon
3	chr11:65460400-65463000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:65461200-65465000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:65461600-65463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:65461600-65463800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:65461800-65463000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:65461800-65463000	Weak transcription	Pancreas	Pancrea
9	chr11:65461800-65465600	Weak transcription	K562	blood
10	chr11:65462000-65463000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:65462000-65463000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:65462000-65463400	Weak transcription	Right Atrium	heart
13	chr11:65462000-65465600	Weak transcription	Esophagus	oesophagus
14	chr11:65462000-65465800	Weak transcription	Gastric	stomach
15	chr11:65462400-65468000	Enhancers	Brain Hippocampus Middle	brain
16	chr11:65462600-65463000	Enhancers	Brain Anterior Caudate	brain
17	chr11:65462600-65464400	Enhancers	Brain Cingulate Gyrus	brain
18	chr11:65462600-65464600	Enhancers	Brain Substantia Nigra	brain
19	chr11:65462600-65467800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr11:65462800-65463000	Bivalent Enhancer	HepG2	liver
21	chr11:65462800-65463800	Enhancers	Colon Smooth Muscle	Colon
22	chr11:65462800-65463800	Enhancers	Rectal Mucosa Donor 31	rectum

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