Variant report

Variant	rs11607554
Chromosome Location	chr11:86376341-86376342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86368500..86371397-chr11:86375081..86378008,3	MCF-7	breast:
2	chr11:86375294..86378539-chr11:86378821..86381383,4	MCF-7	breast:
3	chr11:86374935..86377695-chr11:86510735..86513709,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10501627	1.00[CEU][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10501628	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10792868	0.89[ASN][1000 genomes]
rs10898524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10898525	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11234708	0.92[CEU][hapmap]
rs11234727	0.94[ASN][1000 genomes]
rs11494278	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11512936	0.89[ASN][1000 genomes]
rs11512938	0.84[ASN][1000 genomes]
rs11518768	0.89[ASN][1000 genomes]
rs11518769	0.89[ASN][1000 genomes]
rs11606017	1.00[CEU][hapmap]
rs12361283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12362293	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12790474	1.00[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12804997	0.92[CEU][hapmap]
rs1540083	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1938918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1938919	0.89[ASN][1000 genomes]
rs1938920	0.89[ASN][1000 genomes]
rs1938922	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4291698	0.91[ASN][1000 genomes]
rs4944614	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4944616	0.89[ASN][1000 genomes]
rs4944617	0.89[ASN][1000 genomes]
rs7104141	0.89[ASN][1000 genomes]
rs9943611	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11607554	ME3	cis	multi-tissue	Pritchard
rs11607554	CCDC90B	cis	parietal	SCAN
rs11607554	CTSC	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86362000-86378000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:86366200-86380000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:86366600-86379800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:86369800-86379600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:86369800-86379600	Weak transcription	Lung	lung
6	chr11:86369800-86379800	Weak transcription	Brain Anterior Caudate	brain
7	chr11:86369800-86381200	Weak transcription	Pancreas	Pancrea
8	chr11:86369800-86382000	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:86370000-86382000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:86370400-86379600	Weak transcription	Fetal Brain Female	brain
11	chr11:86370600-86379400	Weak transcription	Fetal Brain Male	brain
12	chr11:86371200-86380800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:86371400-86378600	Weak transcription	Osteobl	bone
14	chr11:86371400-86379600	Weak transcription	Right Atrium	heart
15	chr11:86371400-86381000	Weak transcription	HUVEC	blood vessel
16	chr11:86371400-86381000	Weak transcription	NHLF	lung
17	chr11:86371400-86381200	Weak transcription	Stomach Mucosa	stomach
18	chr11:86371400-86381400	Weak transcription	HSMM	muscle
19	chr11:86371600-86376400	Weak transcription	NHEK	skin
20	chr11:86371600-86380800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:86371800-86378600	Weak transcription	Fetal Lung	lung
22	chr11:86372400-86376400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:86372400-86381200	Weak transcription	NHDF-Ad	bronchial
24	chr11:86372800-86377000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:86372800-86379600	Weak transcription	Brain Angular Gyrus	brain
26	chr11:86373000-86381200	Weak transcription	Primary T cells from cord blood	blood
27	chr11:86373000-86381200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:86373600-86382000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:86373800-86376800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:86374000-86376400	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:86374400-86376600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:86374600-86377600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:86374600-86380200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:86374600-86380200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:86374600-86381200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:86374600-86381200	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:86374800-86381000	Weak transcription	Adipose Nuclei	Adipose
38	chr11:86374800-86381200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:86375400-86376800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:86375400-86376800	Genic enhancers	A549	lung
41	chr11:86375600-86376600	Strong transcription	Fetal Stomach	stomach
42	chr11:86375600-86376800	Genic enhancers	Left Ventricle	heart
43	chr11:86375800-86376400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:86375800-86376800	Genic enhancers	Right Ventricle	heart
45	chr11:86375800-86379600	Weak transcription	Brain Germinal Matrix	brain
46	chr11:86375800-86380200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:86375800-86380200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:86375800-86382000	Weak transcription	Fetal Intestine Small	intestine
49	chr11:86376000-86376600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:86376000-86378000	Weak transcription	Psoas Muscle	Psoas

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