Variant report

Variant	rs28481863
Chromosome Location	chr12:123902361-123902362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123899774..123903276-chr12:123906131..123908571,3	K562	blood:
2	chr12:123745148..123747831-chr12:123900027..123902729,2	K562	blood:
3	chr12:123900528..123903276-chr12:123907055..123908571,2	K562	blood:

Variant related genes	Relation type
ENSG00000269980	Chromatin interaction
ENSG00000235423	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs28372579	0.84[EUR][1000 genomes]
rs28376121	0.92[EUR][1000 genomes]
rs28406193	0.87[EUR][1000 genomes]
rs28410896	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28472704	0.87[EUR][1000 genomes]
rs28569885	0.95[EUR][1000 genomes]
rs28576953	0.87[EUR][1000 genomes]
rs28625019	0.98[EUR][1000 genomes]
rs28636834	0.81[EUR][1000 genomes]
rs28676499	0.98[EUR][1000 genomes]
rs28706696	0.98[EUR][1000 genomes]
rs28715490	0.98[EUR][1000 genomes]
rs28855757	0.85[EUR][1000 genomes]
rs4930718	0.86[EUR][1000 genomes]
rs4930719	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers 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 miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28481863	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28481863	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28481863	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28481863	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28481863	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28481863	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28481863	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123889600-123902600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:123889600-123917000	Weak transcription	K562	blood
4	chr12:123889800-123902800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
6	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
7	chr12:123891400-123908600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
10	chr12:123892000-123903800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:123892000-123911400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:123892200-123905200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:123892200-123905200	Weak transcription	Brain Angular Gyrus	brain
14	chr12:123892200-123905200	Weak transcription	HMEC	breast
15	chr12:123892200-123910000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:123892200-123916800	Weak transcription	NHEK	skin
17	chr12:123892200-123920200	Weak transcription	NH-A	brain
18	chr12:123892600-123907000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:123893400-123905200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
22	chr12:123893600-123905200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:123893600-123905200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:123893800-123905200	Weak transcription	Gastric	stomach
25	chr12:123893800-123908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:123893800-123909600	Weak transcription	Brain Germinal Matrix	brain
27	chr12:123894000-123907800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
29	chr12:123894200-123905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:123894200-123905400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:123894200-123908000	Weak transcription	Fetal Intestine Large	intestine
32	chr12:123894200-123911600	Weak transcription	Esophagus	oesophagus
33	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
35	chr12:123894400-123905200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:123894400-123905200	Weak transcription	Osteobl	bone
37	chr12:123894400-123907000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:123894800-123908200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:123894800-123911600	Weak transcription	Colonic Mucosa	Colon
40	chr12:123894800-123920000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:123895000-123905200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:123895000-123905800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:123895000-123907200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:123895200-123904600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123895200-123905200	Weak transcription	Right Ventricle	heart
46	chr12:123895200-123905400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:123895200-123905800	Weak transcription	NHDF-Ad	bronchial
48	chr12:123895200-123907000	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:123895200-123911600	Weak transcription	Fetal Lung	lung
50	chr12:123895200-123918200	Weak transcription	Pancreas	Pancrea

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