Variant report

Variant	rs12827275
Chromosome Location	chr12:31783007-31783008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31776560..31779005-chr12:31780696..31784088,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11051507	0.81[TSI][hapmap]
rs11051508	0.81[TSI][hapmap]
rs12826630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374165	0.81[TSI][hapmap]
rs34229621	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844104	0.82[EUR][1000 genomes]
rs498080	0.87[ASN][1000 genomes]
rs6487998	0.81[TSI][hapmap]
rs73088360	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967518	0.87[EUR][1000 genomes]
rs7975536	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979755	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12827275	PTHLH	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31782200-31783400	Enhancers	Fetal Intestine Small	intestine
2	chr12:31782200-31783400	Enhancers	Fetal Lung	lung
3	chr12:31782200-31783400	Enhancers	HepG2	liver
4	chr12:31782200-31783600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:31782200-31784600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:31782400-31783200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:31782400-31783200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:31782400-31783200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr12:31782400-31783400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:31782400-31783400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:31782400-31783400	Enhancers	Psoas Muscle	Psoas
12	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:31782400-31783600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:31782400-31783600	Enhancers	Pancreas	Pancrea
16	chr12:31782400-31783600	Enhancers	Right Ventricle	heart
17	chr12:31782400-31783800	Enhancers	Adipose Nuclei	Adipose
18	chr12:31782400-31783800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:31782400-31784000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:31782400-31784000	Enhancers	Fetal Stomach	stomach
21	chr12:31782400-31784000	Enhancers	Left Ventricle	heart
22	chr12:31782400-31784000	Enhancers	HSMM	muscle
23	chr12:31782400-31784600	Enhancers	Fetal Muscle Leg	muscle
24	chr12:31782600-31783200	Enhancers	Right Atrium	heart
25	chr12:31782600-31783400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:31782600-31783400	Flanking Active TSS	Fetal Heart	heart
27	chr12:31782600-31783400	Enhancers	Placenta	Placenta
28	chr12:31782600-31783600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:31782600-31783600	Enhancers	HUVEC	blood vessel
30	chr12:31782800-31783200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr12:31782800-31783200	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr12:31782800-31783400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:31782800-31783600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr12:31782800-31783600	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr12:31783000-31783200	Flanking Active TSS	Fetal Kidney	kidney
36	chr12:31783000-31783200	Enhancers	Rectal Smooth Muscle	rectum
37	chr12:31783000-31783200	Enhancers	K562	blood
38	chr12:31783000-31783200	Flanking Active TSS	NH-A	brain
39	chr12:31783000-31783400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:31783000-31783400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:31783000-31783400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:31783000-31783400	Active TSS	Ovary	ovary
43	chr12:31783000-31783400	Flanking Active TSS	HSMMtube	muscle
44	chr12:31783000-31783400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr12:31783000-31783400	Flanking Active TSS	Osteobl	bone
46	chr12:31783000-31783600	Enhancers	Fetal Muscle Trunk	muscle

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