Variant report

Variant	rs1392455
Chromosome Location	chr5:36300836-36300837
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	chr5:36241131..36242804-chr5:36299171..36301601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152620	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10941287	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741164	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186384	0.82[JPT][hapmap]
rs13161741	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6885584	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs721819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv881598	chr5:36248752-36382802	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1392455	AMACR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36299200-36302400	Weak transcription	Placenta	Placenta
2	chr5:36299200-36302600	Active TSS	Brain Anterior Caudate	brain
3	chr5:36299800-36301400	Enhancers	Colon Smooth Muscle	Colon
4	chr5:36300000-36302000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:36300000-36302000	Flanking Active TSS	Liver	Liver
6	chr5:36300000-36302200	Active TSS	Brain Hippocampus Middle	brain
7	chr5:36300000-36302600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:36300000-36302600	Active TSS	Brain Substantia Nigra	brain
9	chr5:36300000-36303000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:36300000-36303000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:36300000-36303000	Active TSS	Aorta	Aorta
12	chr5:36300200-36301400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:36300200-36301400	Enhancers	Fetal Lung	lung
14	chr5:36300200-36301400	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:36300200-36302000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:36300200-36302400	Active TSS	Brain Cingulate Gyrus	brain
17	chr5:36300200-36302600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr5:36300200-36302600	Active TSS	Right Atrium	heart
19	chr5:36300200-36302800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:36300200-36302800	Active TSS	Brain Angular Gyrus	brain
21	chr5:36300400-36301200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:36300400-36301400	Active TSS	Brain Germinal Matrix	brain
23	chr5:36300400-36301400	Enhancers	Hela-S3	cervix
24	chr5:36300400-36301600	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr5:36300400-36301600	Flanking Active TSS	HSMMtube	muscle
26	chr5:36300400-36301800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr5:36300400-36301800	Enhancers	Fetal Muscle Leg	muscle
28	chr5:36300400-36302000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:36300400-36302000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr5:36300400-36302000	Enhancers	HSMM	muscle
31	chr5:36300400-36302000	Enhancers	NHLF	lung
32	chr5:36300400-36302200	Enhancers	Fetal Stomach	stomach
33	chr5:36300400-36302800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:36300400-36302800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:36300600-36301400	Enhancers	Psoas Muscle	Psoas
36	chr5:36300600-36301400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr5:36300600-36302000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:36300600-36302000	Enhancers	NH-A	brain
39	chr5:36300800-36301000	Enhancers	Ovary	ovary
40	chr5:36300800-36301000	Enhancers	Stomach Smooth Muscle	stomach
41	chr5:36300800-36301200	Flanking Active TSS	Fetal Brain Male	brain
42	chr5:36300800-36301200	Active TSS	Fetal Kidney	kidney
43	chr5:36300800-36301200	Enhancers	NHDF-Ad	bronchial
44	chr5:36300800-36302800	Flanking Active TSS	Osteobl	bone

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