Variant report

Variant	rs12452565
Chromosome Location	chr17:15175027-15175028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PMP22-1	chr17:15174989-15175607	XLOC_012396

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12449310	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12452365	0.82[EUR][1000 genomes]
rs12452683	0.82[EUR][1000 genomes]
rs16951345	0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16951377	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs16951380	0.82[EUR][1000 genomes]
rs16951398	1.00[GIH][hapmap]
rs16951426	1.00[GIH][hapmap]
rs55683203	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56085830	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58893387	0.82[EUR][1000 genomes]
rs7212138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73977995	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73978002	0.82[EUR][1000 genomes]
rs8064719	0.85[AMR][1000 genomes]
rs8069939	0.82[EUR][1000 genomes]
rs8077862	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8079693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8081188	0.96[AMR][1000 genomes];0.91[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	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15169200-15176200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr17:15170600-15175600	Weak transcription	Lung	lung
3	chr17:15172000-15177200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr17:15173000-15176000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:15173000-15176200	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:15173000-15177400	Enhancers	NHDF-Ad	bronchial
7	chr17:15173200-15175800	Enhancers	A549	lung
8	chr17:15173200-15176000	Weak transcription	Placenta	Placenta
9	chr17:15173200-15176200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr17:15173200-15176800	Weak transcription	Right Ventricle	heart
11	chr17:15173200-15177000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:15173200-15192600	Weak transcription	Left Ventricle	heart
13	chr17:15173800-15177400	Enhancers	NHLF	lung
14	chr17:15174000-15176000	Enhancers	HSMMtube	muscle
15	chr17:15174200-15175200	Weak transcription	Adipose Nuclei	Adipose
16	chr17:15174200-15176400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:15174200-15176800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr17:15174200-15177400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:15174400-15175600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:15174400-15176400	Weak transcription	K562	blood
21	chr17:15174400-15177400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:15174800-15175400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:15174800-15176000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr17:15174800-15177800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:15174800-15181600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:15175000-15175400	Flanking Active TSS	Osteobl	bone
27	chr17:15175000-15175800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:15175000-15176800	Enhancers	HSMM	muscle
29	chr17:15175000-15177400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:15175000-15177400	Enhancers	NH-A	brain

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