Variant report

Variant	rs17083248
Chromosome Location	chr4:54517724-54517725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54510430..54512515-chr4:54515785..54518335,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1965112	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17083248	FIP1L1	cis	cerebellum	SCAN
rs17083248	NMU	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54507800-54520600	Weak transcription	Gastric	stomach
2	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
3	chr4:54511400-54520600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:54511600-54518800	Weak transcription	Liver	Liver
5	chr4:54511800-54518400	Weak transcription	GM12878-XiMat	blood
6	chr4:54512600-54518600	Weak transcription	Colonic Mucosa	Colon
7	chr4:54513400-54519600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:54515600-54518800	Enhancers	Esophagus	oesophagus
9	chr4:54515600-54522400	Enhancers	Stomach Mucosa	stomach
10	chr4:54515800-54518600	Active TSS	Adipose Nuclei	Adipose
11	chr4:54515800-54518800	Active TSS	Psoas Muscle	Psoas
12	chr4:54515800-54518800	Active TSS	Right Atrium	heart
13	chr4:54515800-54520800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr4:54515800-54521000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr4:54516000-54518600	Active TSS	Right Ventricle	heart
16	chr4:54516000-54518800	Active TSS	Left Ventricle	heart
17	chr4:54516400-54520600	Weak transcription	Pancreas	Pancrea
18	chr4:54516800-54521000	Enhancers	Fetal Intestine Large	intestine
19	chr4:54517000-54517800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:54517000-54518000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:54517000-54518000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:54517000-54518000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr4:54517000-54518800	Enhancers	Placenta	Placenta
24	chr4:54517000-54518800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr4:54517000-54520200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:54517000-54521000	Enhancers	Fetal Intestine Small	intestine
27	chr4:54517200-54517800	Enhancers	Colon Smooth Muscle	Colon
28	chr4:54517200-54517800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr4:54517200-54518000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:54517200-54518000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:54517200-54518000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:54517200-54518000	Enhancers	Rectal Smooth Muscle	rectum
33	chr4:54517200-54518000	Enhancers	HSMM	muscle
34	chr4:54517400-54517800	Enhancers	HMEC	breast
35	chr4:54517400-54517800	Flanking Active TSS	NHEK	skin
36	chr4:54517400-54518000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:54517400-54518000	Enhancers	HSMMtube	muscle
38	chr4:54517400-54518400	Weak transcription	Small Intestine	intestine
39	chr4:54517400-54518600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr4:54517400-54519000	Enhancers	Fetal Muscle Leg	muscle
41	chr4:54517600-54517800	Enhancers	Fetal Lung	lung
42	chr4:54517600-54518400	Weak transcription	Lung	lung
43	chr4:54517600-54518600	Active TSS	Stomach Smooth Muscle	stomach
44	chr4:54517600-54523200	Weak transcription	Spleen	Spleen

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