Variant report

Variant	rs1366
Chromosome Location	chr12:21669027-21669028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21667585..21669254-chr12:21672387..21674128,2	K562	blood:
2	chr12:21654128..21656631-chr12:21667062..21669279,3	MCF-7	breast:
3	chr12:21666099..21668505-chr12:21668536..21671439,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1048617	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743416	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs10770819	0.83[GIH][hapmap]
rs10841834	0.85[CHD][hapmap]
rs10841841	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11046101	0.94[ASN][1000 genomes]
rs11612017	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs12318289	0.94[CHB][hapmap]
rs12582513	0.82[YRI][hapmap]
rs12582514	0.81[YRI][hapmap]
rs12582538	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]
rs2284392	0.81[CHD][hapmap]
rs3213212	0.86[CHB][hapmap]
rs4565955	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487233	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs768833	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv528556	chr12:21664879-21680363	Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1366	RECQL	cis	cerebellum	SCAN
rs1366	PYROXD1	cis	cerebellum	SCAN
rs1366	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs1366	PYROXD1	cis	Nerve Tibial	GTEx
rs1366	LOC642732	trans	multi-tissue	Pritchard
rs1366	PYROXD1	cis	lung	GTEx
rs1366	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs1366	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs1366	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs1366	PYROXD1	cis	Esophagus Muscularis	GTEx
rs1366	FLJ22028	cis	normal skin	skin_eQTL
rs1366	PYROXD1	cis	parietal	SCAN

Chromatin state (count:117 , 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	chr12:21656000-21671800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
6	chr12:21656200-21669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:21656200-21671800	Weak transcription	Thymus	Thymus
8	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
9	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
10	chr12:21656600-21669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:21656800-21671400	Weak transcription	Fetal Heart	heart
12	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:21657400-21669800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:21657600-21669600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
17	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
18	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
19	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:21657600-21680400	Weak transcription	Gastric	stomach
21	chr12:21660000-21669400	Strong transcription	Placenta	Placenta
22	chr12:21660000-21670400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:21660000-21671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:21660000-21672000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:21660200-21671600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:21660200-21672600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:21660400-21671600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:21660400-21672200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:21660600-21669400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:21660600-21669400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:21660600-21669600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:21660600-21669600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:21660600-21670400	Strong transcription	HUVEC	blood vessel
34	chr12:21660600-21670800	Strong transcription	Osteobl	bone
35	chr12:21660600-21672600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:21660800-21670000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:21660800-21670400	Strong transcription	Dnd41	blood
38	chr12:21660800-21671600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:21660800-21672400	Strong transcription	Liver	Liver
40	chr12:21661000-21670600	Strong transcription	Adipose Nuclei	Adipose
41	chr12:21661400-21670800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:21662200-21672400	Strong transcription	HSMM	muscle
44	chr12:21663400-21671000	Strong transcription	GM12878-XiMat	blood
45	chr12:21663600-21669400	Strong transcription	Hela-S3	cervix
46	chr12:21664400-21669800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:21664400-21671800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:21664600-21670600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:21664800-21669400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:21664800-21671600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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