Variant report

Variant	rs11227771
Chromosome Location	chr11:67103602-67103603
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	chr11:67019702..67021947-chr11:67103039..67105816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173120	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10732253	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs10896171	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11227764	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11826923	1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1253784	1.00[GIH][hapmap]
rs2004225	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2066491	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2228522	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2255990	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2276020	1.00[MEX][hapmap]
rs3741189	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs3802745	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825022	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4457752	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs57238619	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58530946	0.90[EUR][1000 genomes]
rs60229295	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61891566	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61891569	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61891571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645387	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs682509	1.00[GIH][hapmap]
rs72932705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
5	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv468603	chr11:67033076-67164495	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv555253	chr11:67033076-67164495	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
9	nsv1047890	chr11:67058231-67184436	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
11	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11227771	NA	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67086000-67104400	Weak transcription	Aorta	Aorta
2	chr11:67086200-67113600	Weak transcription	Osteobl	bone
3	chr11:67086400-67104000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:67086400-67110200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:67086400-67111200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:67086400-67111600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:67086400-67112600	Weak transcription	Fetal Lung	lung
8	chr11:67086400-67120000	Weak transcription	Brain Germinal Matrix	brain
9	chr11:67086600-67103800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:67086600-67111200	Weak transcription	Primary B cells from cord blood	blood
11	chr11:67086600-67111200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:67086600-67118400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:67086800-67118800	Weak transcription	Fetal Brain Male	brain
14	chr11:67087000-67111800	Weak transcription	Gastric	stomach
15	chr11:67087000-67112800	Weak transcription	Hela-S3	cervix
16	chr11:67087000-67113400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:67087800-67113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:67087800-67119000	Weak transcription	Fetal Brain Female	brain
19	chr11:67089400-67116800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:67089800-67117000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:67090000-67118600	Weak transcription	Brain Anterior Caudate	brain
22	chr11:67090200-67115400	Weak transcription	Lung	lung
23	chr11:67090400-67111200	Weak transcription	Spleen	Spleen
24	chr11:67090800-67111800	Weak transcription	Pancreas	Pancrea
25	chr11:67091000-67105800	Weak transcription	Brain Angular Gyrus	brain
26	chr11:67091200-67109400	Weak transcription	Fetal Stomach	stomach
27	chr11:67091400-67112800	Weak transcription	Esophagus	oesophagus
28	chr11:67095000-67105200	Weak transcription	Adipose Nuclei	Adipose
29	chr11:67096400-67111800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:67098600-67111800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:67099200-67118600	Weak transcription	Thymus	Thymus
32	chr11:67099600-67105000	Weak transcription	Left Ventricle	heart
33	chr11:67100600-67107000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:67100600-67113000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:67101000-67112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:67101000-67112600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:67101000-67113600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:67101200-67104200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:67101200-67109200	Weak transcription	Fetal Intestine Small	intestine
40	chr11:67101200-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:67101600-67112600	Weak transcription	Fetal Intestine Large	intestine
42	chr11:67101600-67116400	Weak transcription	Right Ventricle	heart
43	chr11:67101600-67118600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:67101600-67118600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:67101800-67104000	Weak transcription	Ovary	ovary
46	chr11:67101800-67112600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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