Variant report

Variant	rs28755851
Chromosome Location	chr12:123486282-123486283
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123483916..123486728-chr12:123489972..123492834,2	K562	blood:
2	chr12:123479422..123482791-chr12:123483500..123486744,3	K562	blood:
3	chr12:123452570..123455545-chr12:123485965..123487801,2	K562	blood:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10773921	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10848428	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11060853	0.83[ASN][1000 genomes]
rs11608811	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11613937	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425009	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425850	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727307	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1790094	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1790106	0.80[EUR][1000 genomes]
rs1790121	0.80[EUR][1000 genomes]
rs1790122	0.80[EUR][1000 genomes]
rs1984658	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741530	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759115	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3897102	1.00[ASN][1000 genomes]
rs4148862	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148863	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148866	0.83[ASN][1000 genomes]
rs4275659	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55742290	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61955196	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61955214	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7135296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296418	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305511	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957096	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883562	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs884956	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949143	0.80[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28755851	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28755851	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28755851	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28755851	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28755851	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28755851	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 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	chr12:123469400-123491600	Weak transcription	HMEC	breast
5	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
6	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:123469800-123486800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:123469800-123491400	Weak transcription	HSMMtube	muscle
10	chr12:123469800-123491600	Weak transcription	Osteobl	bone
11	chr12:123470000-123486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
14	chr12:123472000-123499000	Strong transcription	Thymus	Thymus
15	chr12:123472400-123491400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:123472600-123492800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:123472800-123494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:123472800-123500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:123473200-123489400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:123473200-123489400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:123473200-123491200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:123473400-123501000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:123473800-123492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:123473800-123500800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:123475600-123491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:123478400-123486800	Strong transcription	Fetal Stomach	stomach
27	chr12:123479800-123489400	Weak transcription	A549	lung
28	chr12:123480800-123487600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:123481200-123486400	Strong transcription	Right Ventricle	heart
30	chr12:123481400-123491800	Weak transcription	HepG2	liver
31	chr12:123481800-123492600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:123482000-123489000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:123482200-123488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:123482400-123489600	Weak transcription	NHEK	skin
35	chr12:123482800-123488800	Weak transcription	Gastric	stomach
36	chr12:123483000-123488800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:123483000-123488800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:123483200-123496800	Weak transcription	Psoas Muscle	Psoas
39	chr12:123484400-123492800	Weak transcription	Brain Substantia Nigra	brain
40	chr12:123484600-123487200	Weak transcription	Brain Angular Gyrus	brain
41	chr12:123485000-123488800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:123485000-123488800	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:123485200-123488800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:123485200-123496200	Strong transcription	Fetal Thymus	thymus
45	chr12:123485400-123486400	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:123485400-123489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:123485600-123487400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:123485600-123487800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:123485600-123488200	Weak transcription	Colonic Mucosa	Colon
50	chr12:123485600-123488800	Weak transcription	Aorta	Aorta

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