Variant report

Variant	rs12826630
Chromosome Location	chr12:31782588-31782589
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	chr12:31776560..31779005-chr12:31780696..31784088,3	K562	blood:
2	chr12:31477438..31479159-chr12:31779343..31782901,3	K562	blood:

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction

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]
rs12827275	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374165	0.81[TSI][hapmap]
rs34229621	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844104	0.81[EUR][1000 genomes]
rs498080	0.87[ASN][1000 genomes]
rs6487998	0.81[TSI][hapmap]
rs73088360	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967518	0.86[EUR][1000 genomes]
rs7975536	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979755	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[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
rs12826630	PTHLH	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31773600-31782600	Weak transcription	A549	lung
2	chr12:31781000-31782600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:31781400-31783000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:31782200-31782600	Enhancers	Fetal Heart	heart
5	chr12:31782200-31783000	Enhancers	Fetal Kidney	kidney
6	chr12:31782200-31783400	Enhancers	Fetal Intestine Small	intestine
7	chr12:31782200-31783400	Enhancers	Fetal Lung	lung
8	chr12:31782200-31783400	Enhancers	HepG2	liver
9	chr12:31782200-31783600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:31782200-31784600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:31782400-31782600	Flanking Active TSS	Ovary	ovary
12	chr12:31782400-31782600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr12:31782400-31782800	Enhancers	Colon Smooth Muscle	Colon
14	chr12:31782400-31782800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:31782400-31782800	Enhancers	Spleen	Spleen
16	chr12:31782400-31782800	Enhancers	K562	blood
17	chr12:31782400-31783000	Enhancers	HSMMtube	muscle
18	chr12:31782400-31783000	Enhancers	NHDF-Ad	bronchial
19	chr12:31782400-31783200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:31782400-31783200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:31782400-31783200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr12:31782400-31783400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:31782400-31783400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:31782400-31783400	Enhancers	Psoas Muscle	Psoas
25	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:31782400-31783600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:31782400-31783600	Enhancers	Pancreas	Pancrea
29	chr12:31782400-31783600	Enhancers	Right Ventricle	heart
30	chr12:31782400-31783800	Enhancers	Adipose Nuclei	Adipose
31	chr12:31782400-31783800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:31782400-31784000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:31782400-31784000	Enhancers	Fetal Stomach	stomach
34	chr12:31782400-31784000	Enhancers	Left Ventricle	heart
35	chr12:31782400-31784000	Enhancers	HSMM	muscle
36	chr12:31782400-31784600	Enhancers	Fetal Muscle Leg	muscle

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