Variant report

Variant	rs11234689
Chromosome Location	chr11:86259006-86259007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10898485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11234665	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs11602862	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606745	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12222272	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2051434	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3819227	0.81[CEU][hapmap]
rs58410116	0.86[AMR][1000 genomes]
rs72953621	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv528182	chr11:86234604-86259006	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11234689	FZD4	cis	cerebellum	SCAN
rs11234689	PRSS23	cis	cerebellum	SCAN
rs11234689	PRSS23	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86237800-86262200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:86249800-86261800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr11:86250400-86261600	Weak transcription	Gastric	stomach
4	chr11:86251200-86261600	Weak transcription	Right Ventricle	heart
5	chr11:86256600-86262400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:86257800-86262200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:86258600-86261000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:86258800-86259200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr11:86258800-86259200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr11:86258800-86259200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:86258800-86259200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:86258800-86259400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:86258800-86259400	Enhancers	Brain Angular Gyrus	brain
14	chr11:86258800-86259400	Enhancers	Brain Cingulate Gyrus	brain
15	chr11:86258800-86259400	Enhancers	Fetal Heart	heart
16	chr11:86258800-86259400	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:86258800-86259600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr11:86258800-86259600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr11:86258800-86259600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr11:86258800-86259600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:86258800-86259800	Enhancers	Brain Hippocampus Middle	brain
22	chr11:86258800-86260000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:86258800-86260000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr11:86258800-86260000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:86258800-86260000	Enhancers	Fetal Kidney	kidney
26	chr11:86258800-86260000	Enhancers	Fetal Muscle Leg	muscle
27	chr11:86258800-86260000	Enhancers	Fetal Stomach	stomach
28	chr11:86258800-86260000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr11:86258800-86260000	Enhancers	HMEC	breast
30	chr11:86258800-86260200	Enhancers	Adipose Nuclei	Adipose
31	chr11:86258800-86260200	Enhancers	Brain Anterior Caudate	brain
32	chr11:86258800-86260200	Enhancers	NHEK	skin
33	chr11:86258800-86260400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:86258800-86260400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:86258800-86260400	Enhancers	Aorta	Aorta
36	chr11:86258800-86260800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:86258800-86260800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:86258800-86260800	Enhancers	NHDF-Ad	bronchial
39	chr11:86258800-86260800	Enhancers	NHLF	lung
40	chr11:86258800-86261000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:86258800-86261000	Enhancers	Fetal Brain Female	brain
42	chr11:86258800-86261200	Enhancers	NH-A	brain
43	chr11:86258800-86262200	Enhancers	HUVEC	blood vessel
44	chr11:86258800-86263400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr11:86258800-86263400	Enhancers	Fetal Brain Male	brain
46	chr11:86258800-86263400	Enhancers	Psoas Muscle	Psoas
47	chr11:86258800-86264600	Enhancers	Right Atrium	heart
48	chr11:86259000-86259200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr11:86259000-86259200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:86259000-86259200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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