Variant report

Variant	rs12820906
Chromosome Location	chr12:123493123-123493124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123491668..123493633-chr12:123498579..123500391,2	K562	blood:
2	chr12:123488771..123490816-chr12:123491937..123493627,3	K562	blood:
3	chr12:123492899..123494796-chr12:123502898..123505077,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12811109	0.83[EUR][1000 genomes]
rs12828755	0.83[EUR][1000 genomes]
rs1463877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1617156	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1727294	0.80[ASN][1000 genomes]
rs2270789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2510885	0.80[ASN][1000 genomes]
rs4148856	0.92[ASN][1000 genomes]
rs520088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs585522	0.94[CHB][hapmap]
rs641760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs655293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs71444568	0.80[ASN][1000 genomes]
rs7299943	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs883263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883563	0.89[ASN][1000 genomes]
rs937564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940904	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12820906	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12820906	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12820906	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12820906	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs12820906	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
2	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
3	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
4	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
5	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
9	chr12:123472000-123499000	Strong transcription	Thymus	Thymus
10	chr12:123472800-123494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:123472800-123500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:123473400-123501000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:123473800-123500800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:123483200-123496800	Weak transcription	Psoas Muscle	Psoas
15	chr12:123485200-123496200	Strong transcription	Fetal Thymus	thymus
16	chr12:123485600-123495600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:123485800-123493200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr12:123487400-123497600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:123487600-123498800	Strong transcription	Fetal Stomach	stomach
20	chr12:123488000-123497400	Strong transcription	Ovary	ovary
21	chr12:123488000-123498400	Strong transcription	Right Ventricle	heart
22	chr12:123488000-123498800	Strong transcription	Fetal Intestine Small	intestine
23	chr12:123488200-123494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:123488400-123498600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:123488600-123498600	Strong transcription	Liver	Liver
26	chr12:123488800-123498400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:123489200-123512400	Weak transcription	Aorta	Aorta
28	chr12:123490000-123493400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:123490000-123494000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:123490000-123495600	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:123490000-123515800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:123490200-123493800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:123490200-123494000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:123490200-123494000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123490200-123498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:123490200-123503600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:123490200-123511000	Weak transcription	Pancreas	Pancrea
38	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:123490400-123493200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:123490400-123493600	Weak transcription	Fetal Intestine Large	intestine
41	chr12:123490400-123503200	Weak transcription	NHEK	skin
42	chr12:123490400-123503800	Weak transcription	A549	lung
43	chr12:123491200-123494400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:123491200-123498400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:123491200-123498800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:123491200-123503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:123491400-123495000	Strong transcription	Brain Angular Gyrus	brain
48	chr12:123491400-123498400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:123491400-123498400	Strong transcription	Adipose Nuclei	Adipose
50	chr12:123491400-123498600	Strong transcription	Skeletal Muscle Male	skeletal muscle

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