Variant report

Variant	rs12582538
Chromosome Location	chr12:21663619-21663620
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21653310..21655607-chr12:21663313..21666443,3	K562	blood:
2	chr12:21659539..21661221-chr12:21663545..21665442,3	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1048617	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743416	0.86[CHB][hapmap]
rs10841841	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046101	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612017	0.86[CHB][hapmap]
rs12318289	0.89[CHB][hapmap]
rs13035	0.81[CEU][hapmap]
rs1366	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3213212	0.83[CHB][hapmap]
rs4565955	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487233	0.81[CHB][hapmap]
rs768833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12582538	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs12582538	FLJ22028	cis	normal skin	skin_eQTL
rs12582538	PYROXD1	cis	Esophagus Muscularis	GTEx
rs12582538	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs12582538	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs12582538	PYROXD1	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21655600-21666000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:21656000-21671800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
7	chr12:21656200-21664000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:21656200-21665000	Weak transcription	HSMMtube	muscle
9	chr12:21656200-21665200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:21656200-21665600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:21656200-21666200	Weak transcription	Colonic Mucosa	Colon
12	chr12:21656200-21669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:21656200-21671800	Weak transcription	Thymus	Thymus
14	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
15	chr12:21656400-21668000	Weak transcription	Fetal Lung	lung
16	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
17	chr12:21656600-21663800	Weak transcription	NHLF	lung
18	chr12:21656600-21665200	Weak transcription	NHEK	skin
19	chr12:21656600-21665400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:21656600-21665800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:21656600-21669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:21656800-21665800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:21656800-21666000	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:21656800-21666600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:21656800-21671400	Weak transcription	Fetal Heart	heart
26	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:21657400-21665800	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:21657400-21669800	Weak transcription	Brain Substantia Nigra	brain
29	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:21657600-21663800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:21657600-21665600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:21657600-21665800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:21657600-21665800	Weak transcription	Esophagus	oesophagus
34	chr12:21657600-21665800	Weak transcription	Lung	lung
35	chr12:21657600-21665800	Weak transcription	Ovary	ovary
36	chr12:21657600-21666400	Weak transcription	Psoas Muscle	Psoas
37	chr12:21657600-21666400	Weak transcription	Spleen	Spleen
38	chr12:21657600-21669600	Weak transcription	Brain Angular Gyrus	brain
39	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
40	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
41	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
42	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:21657600-21680400	Weak transcription	Gastric	stomach
44	chr12:21658000-21663800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:21658000-21665600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:21658600-21666400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:21659200-21664400	Weak transcription	Brain Anterior Caudate	brain
48	chr12:21660000-21669400	Strong transcription	Placenta	Placenta
49	chr12:21660000-21670400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:21660000-21671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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