Variant report

Variant	rs28676499
Chromosome Location	chr12:123906307-123906308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123899774..123903276-chr12:123906131..123908571,3	K562	blood:
2	chr12:123905727..123907449-chr12:124100354..124102343,2	K562	blood:

Variant related genes	Relation type
ENSG00000206897	Chromatin interaction
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12299125	0.80[EUR][1000 genomes]
rs28372579	0.85[EUR][1000 genomes]
rs28376121	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28406193	0.88[EUR][1000 genomes]
rs28410896	0.90[EUR][1000 genomes]
rs28458312	0.80[EUR][1000 genomes]
rs28472704	0.88[EUR][1000 genomes]
rs28481863	0.98[EUR][1000 genomes]
rs28569885	0.95[EUR][1000 genomes]
rs28576953	0.88[EUR][1000 genomes]
rs28583837	0.80[EUR][1000 genomes]
rs28625019	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636834	0.82[EUR][1000 genomes]
rs28706696	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715490	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28855757	0.85[EUR][1000 genomes]
rs4930718	0.88[EUR][1000 genomes]
rs4930719	0.95[AMR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28676499	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28676499	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28676499	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28676499	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28676499	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 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	chr12:123889600-123917000	Weak transcription	K562	blood
3	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
4	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
5	chr12:123891400-123908600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
8	chr12:123892000-123911400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:123892200-123910000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:123892200-123916800	Weak transcription	NHEK	skin
11	chr12:123892200-123920200	Weak transcription	NH-A	brain
12	chr12:123892600-123907000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
15	chr12:123893800-123908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:123893800-123909600	Weak transcription	Brain Germinal Matrix	brain
17	chr12:123894000-123907800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
19	chr12:123894200-123908000	Weak transcription	Fetal Intestine Large	intestine
20	chr12:123894200-123911600	Weak transcription	Esophagus	oesophagus
21	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
23	chr12:123894400-123907000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:123894800-123908200	Weak transcription	Fetal Intestine Small	intestine
25	chr12:123894800-123911600	Weak transcription	Colonic Mucosa	Colon
26	chr12:123894800-123920000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:123895000-123907200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:123895200-123907000	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:123895200-123911600	Weak transcription	Fetal Lung	lung
30	chr12:123895200-123918200	Weak transcription	Pancreas	Pancrea
31	chr12:123895200-123920000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:123895200-123920000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:123895200-123920000	Weak transcription	HSMM	muscle
34	chr12:123895200-123920000	Weak transcription	NHLF	lung
35	chr12:123895200-123920200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:123895200-123920200	Weak transcription	A549	lung
37	chr12:123895400-123911600	Weak transcription	Brain Substantia Nigra	brain
38	chr12:123896200-123909400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:123896200-123911800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:123896200-123915600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:123896200-123915800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:123896400-123916200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:123896600-123908000	Strong transcription	Lung	lung
44	chr12:123897000-123908000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:123898400-123909600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:123899000-123907600	Strong transcription	Spleen	Spleen
47	chr12:123899400-123907800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:123899400-123908600	Strong transcription	Fetal Stomach	stomach
49	chr12:123899400-123909400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:123899600-123906400	Strong transcription	GM12878-XiMat	blood

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