Variant report

Variant	rs571006
Chromosome Location	chr11:86392623-86392624
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	chr11:86386748..86389830-chr11:86391852..86394746,3	MCF-7	breast:
2	chr11:86392536..86395148-chr11:86403712..86405741,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10792865	1.00[CEU][hapmap]
rs2508305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2513017	0.88[CEU][hapmap]
rs4592448	1.00[CEU][hapmap]
rs546427	0.85[CEU][hapmap]
rs567615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs597823	0.89[EUR][1000 genomes]
rs61904321	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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	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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs571006	FZD4	cis	parietal	SCAN
rs571006	PODXL	trans	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86383800-86393000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:86383800-86393200	Weak transcription	Aorta	Aorta
3	chr11:86384800-86393200	Weak transcription	Pancreas	Pancrea
4	chr11:86384800-86397800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:86384800-86400400	Weak transcription	Gastric	stomach
6	chr11:86385200-86411400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:86386600-86431000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:86387000-86392800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:86388000-86409600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:86389600-86397800	Weak transcription	Fetal Muscle Leg	muscle
11	chr11:86389800-86393200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:86389800-86399600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:86390000-86403600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:86390200-86398600	Weak transcription	Osteobl	bone
15	chr11:86390200-86399800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:86390400-86398000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:86390400-86399800	Weak transcription	Fetal Kidney	kidney
18	chr11:86390600-86397800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:86391200-86393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:86391200-86393800	Enhancers	Psoas Muscle	Psoas
21	chr11:86391400-86392800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:86391400-86392800	Enhancers	Fetal Intestine Small	intestine
23	chr11:86391400-86393400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:86391400-86393800	Enhancers	Ovary	ovary
25	chr11:86391400-86394400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr11:86391400-86395200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:86391600-86393800	Enhancers	Right Ventricle	heart
28	chr11:86391600-86394000	Enhancers	Colon Smooth Muscle	Colon
29	chr11:86391800-86393000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:86391800-86399400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:86392000-86393600	Enhancers	Fetal Lung	lung
32	chr11:86392000-86393600	Enhancers	Rectal Smooth Muscle	rectum
33	chr11:86392200-86393000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:86392200-86399600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:86392400-86392800	Weak transcription	Left Ventricle	heart
36	chr11:86392400-86392800	Weak transcription	Right Atrium	heart
37	chr11:86392400-86393400	Enhancers	Fetal Stomach	stomach
38	chr11:86392400-86393600	Enhancers	Fetal Heart	heart
39	chr11:86392600-86393000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:86392600-86393200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:86392600-86393200	Enhancers	Duodenum Mucosa	Duodenum
42	chr11:86392600-86393400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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