Variant report

Variant	rs11235005
Chromosome Location	chr11:86889351-86889352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11234994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235078	1.00[JPT][hapmap]
rs12364798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128894	1.00[JPT][hapmap]
rs7936587	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv468777	chr11:86794856-86985581	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv555707	chr11:86794856-86985581	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv898060	chr11:86822077-86912633	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv420	chr11:86845328-86890111	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv898061	chr11:86850483-86944982	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv468778	chr11:86850483-86974576	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv555708	chr11:86850483-86974576	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv898062	chr11:86864277-86902079	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv898063	chr11:86864277-86944982	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv518332	chr11:86889284-86891077	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv525787	chr11:86889284-86920178	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11235005	APLP1	trans	lymphoblastoid	seeQTL
rs11235005	RCN3	trans	lymphoblastoid	seeQTL
rs11235005	FGFBP2	trans	lymphoblastoid	seeQTL
rs11235005	RALGPS2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86880600-86891800	Weak transcription	Aorta	Aorta
2	chr11:86880800-86892600	Weak transcription	Liver	Liver
3	chr11:86881800-86891000	Weak transcription	Thymus	Thymus
4	chr11:86882000-86928000	Weak transcription	Left Ventricle	heart
5	chr11:86884400-86891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:86884600-86896600	Weak transcription	Fetal Kidney	kidney
7	chr11:86884600-86899200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:86884800-86901200	Weak transcription	K562	blood
9	chr11:86885000-86892000	Weak transcription	Brain Substantia Nigra	brain
10	chr11:86885000-86893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:86885000-86902200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:86885200-86890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:86885200-86891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:86885400-86891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:86885800-86889600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:86885800-86891800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:86886200-86889600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:86886200-86894800	Weak transcription	Fetal Heart	heart
19	chr11:86886400-86896600	Weak transcription	Adipose Nuclei	Adipose
20	chr11:86886600-86891000	Weak transcription	HSMMtube	muscle
21	chr11:86886600-86891600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:86886800-86890400	Weak transcription	HepG2	liver
23	chr11:86887400-86889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:86887400-86891800	Weak transcription	Ovary	ovary
25	chr11:86887400-86899600	Weak transcription	NHDF-Ad	bronchial
26	chr11:86887600-86890000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:86887600-86890200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:86887600-86893800	Weak transcription	NHLF	lung
29	chr11:86887600-86909400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:86888000-86889400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:86888000-86891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:86888400-86889400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:86888600-86889600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:86888600-86889800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:86888800-86889400	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr11:86888800-86889800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:86888800-86889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:86888800-86889800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr11:86888800-86889800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr11:86888800-86889800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:86888800-86891600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:86889000-86889600	Strong transcription	Primary B cells from cord blood	blood
43	chr11:86889000-86889600	ZNF genes & repeats	A549	lung
44	chr11:86889000-86889800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:86889000-86889800	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr11:86889000-86891600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:86889200-86889800	ZNF genes & repeats	Fetal Lung	lung
48	chr11:86889200-86889800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
49	chr11:86889200-86890400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr11:86889200-86891800	Weak transcription	Stomach Smooth Muscle	stomach

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