Variant report

Variant	rs2284395
Chromosome Location	chr12:21651460-21651461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21629758..21631544-chr12:21651304..21653537,2	MCF-7	breast:
2	chr12:21632020..21637029-chr12:21648453..21652691,4	K562	blood:
3	chr12:21642768..21647284-chr12:21648642..21652273,4	K562	blood:
4	chr12:21650395..21652297-chr12:21809940..21812051,2	K562	blood:

Variant related genes	Relation type
ENSG00000111716	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10492117	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10841835	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841836	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10841837	0.92[EUR][1000 genomes]
rs11046089	0.83[ASN][1000 genomes]
rs12231436	0.91[ASN][1000 genomes]
rs12423412	0.91[ASN][1000 genomes]
rs12822436	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12829302	0.91[ASN][1000 genomes]
rs12833589	0.91[ASN][1000 genomes]
rs2110159	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284393	0.86[ASN][1000 genomes]
rs2284394	0.98[ASN][1000 genomes]
rs2300211	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2300212	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2417991	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34965831	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35538394	0.91[EUR][1000 genomes]
rs3782661	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4762834	0.83[ASN][1000 genomes]
rs4762835	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61926332	0.80[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2284395	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2284395	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs2284395	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs2284395	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
2	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
3	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
5	chr12:21619800-21652200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:21619800-21652400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:21619800-21652400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:21620200-21652600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:21620600-21652200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:21630400-21652000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:21630400-21652400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:21636200-21652800	Weak transcription	K562	blood
13	chr12:21636400-21653400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:21636400-21653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:21640000-21652200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:21640000-21652400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:21640400-21652000	Strong transcription	Adipose Nuclei	Adipose
18	chr12:21640400-21652200	Strong transcription	Osteobl	bone
19	chr12:21640400-21652400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:21640400-21652400	Strong transcription	Placenta	Placenta
21	chr12:21640600-21651600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:21640600-21651600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:21640600-21651600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:21640600-21651600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:21640600-21651800	Strong transcription	Primary T cells from cord blood	blood
26	chr12:21640600-21651800	Strong transcription	HSMM	muscle
27	chr12:21640600-21652000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:21640600-21652200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:21640600-21652200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:21640600-21652200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:21640600-21652400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:21640600-21652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:21640800-21651600	Strong transcription	Liver	Liver
34	chr12:21640800-21651600	Strong transcription	Fetal Thymus	thymus
35	chr12:21640800-21651800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:21641000-21652200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:21641200-21652200	Strong transcription	HMEC	breast
38	chr12:21641400-21651600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:21641400-21652600	Weak transcription	Fetal Heart	heart
40	chr12:21641800-21652200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:21643800-21651800	Strong transcription	Dnd41	blood
42	chr12:21644200-21652200	Strong transcription	NH-A	brain
43	chr12:21644600-21652000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:21644600-21652200	Strong transcription	NHDF-Ad	bronchial
45	chr12:21644800-21651800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:21644800-21652400	Strong transcription	Primary B cells from cord blood	blood
47	chr12:21644800-21652400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:21645400-21651600	Strong transcription	Brain Germinal Matrix	brain
49	chr12:21645400-21651600	Strong transcription	Fetal Lung	lung
50	chr12:21645400-21652000	Strong transcription	NHLF	lung

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