Variant report

Variant	rs1790119
Chromosome Location	chr12:123615098-123615099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123613552..123616142-chr12:123624690..123626588,2	K562	blood:
2	chr12:123609913..123612055-chr12:123613874..123616292,2	K562	blood:
3	chr12:123610238..123613639-chr12:123613854..123616666,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1047158	0.83[EUR][1000 genomes]
rs1051431	0.82[EUR][1000 genomes]
rs1106240	0.81[EUR][1000 genomes]
rs1106241	0.82[EUR][1000 genomes]
rs1569068	0.84[EUR][1000 genomes]
rs1616131	0.84[EUR][1000 genomes]
rs1616181	0.84[EUR][1000 genomes]
rs1617156	0.85[ASN][1000 genomes]
rs1618679	0.81[AFR][1000 genomes]
rs1621194	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1627724	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1716165	0.82[EUR][1000 genomes]
rs1716167	0.82[EUR][1000 genomes]
rs1716168	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1716185	0.82[EUR][1000 genomes]
rs1727294	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1727296	0.82[EUR][1000 genomes]
rs1727314	0.84[EUR][1000 genomes]
rs1727315	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1727316	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1727317	0.82[EUR][1000 genomes]
rs1727318	0.80[EUR][1000 genomes]
rs1790090	0.83[EUR][1000 genomes]
rs1790108	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1790109	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1790116	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1790120	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2510885	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682429	0.83[EUR][1000 genomes]
rs2695481	0.83[EUR][1000 genomes]
rs2695482	0.82[EUR][1000 genomes]
rs2851438	0.83[EUR][1000 genomes]
rs2851441	0.84[EUR][1000 genomes]
rs655293	0.81[ASN][1000 genomes]
rs7299943	0.85[ASN][1000 genomes]
rs884548	0.83[EUR][1000 genomes]
rs949142	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790119	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1790119	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790119	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790119	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1790119	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1790119	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790119	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
3	chr12:123601600-123615800	Weak transcription	Pancreas	Pancrea
4	chr12:123605000-123616000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:123605800-123624400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123607600-123619600	Genic enhancers	Fetal Thymus	thymus
7	chr12:123610000-123620400	Enhancers	Placenta	Placenta
8	chr12:123611000-123617400	Enhancers	Primary B cells from cord blood	blood
9	chr12:123611400-123616200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:123611400-123624400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:123611600-123615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:123611600-123616200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:123611600-123616600	Weak transcription	Liver	Liver
14	chr12:123611600-123617400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:123611800-123615200	Weak transcription	Fetal Heart	heart
16	chr12:123611800-123615400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:123611800-123615600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:123611800-123616000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:123611800-123616000	Weak transcription	Brain Angular Gyrus	brain
23	chr12:123611800-123616200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:123611800-123616200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:123611800-123616200	Weak transcription	Psoas Muscle	Psoas
26	chr12:123611800-123616200	Weak transcription	Small Intestine	intestine
27	chr12:123611800-123616600	Weak transcription	GM12878-XiMat	blood
28	chr12:123611800-123618000	Enhancers	A549	lung
29	chr12:123611800-123624400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:123611800-123624400	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:123611800-123624600	Weak transcription	Aorta	Aorta
32	chr12:123612000-123615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:123612000-123615400	Weak transcription	Lung	lung
34	chr12:123612000-123615400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:123612000-123615400	Weak transcription	Hela-S3	cervix
36	chr12:123612000-123615600	Weak transcription	Right Ventricle	heart
37	chr12:123612000-123616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:123612000-123616000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:123612000-123616000	Weak transcription	Brain Anterior Caudate	brain
40	chr12:123612000-123616000	Weak transcription	Gastric	stomach
41	chr12:123612000-123616000	Weak transcription	K562	blood
42	chr12:123612000-123616200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:123612000-123616200	Weak transcription	Right Atrium	heart
44	chr12:123612000-123616200	Weak transcription	Stomach Mucosa	stomach
45	chr12:123612000-123617400	Weak transcription	HepG2	liver
46	chr12:123612000-123618600	Weak transcription	Fetal Intestine Small	intestine
47	chr12:123612000-123624000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:123612000-123624600	Weak transcription	NH-A	brain
49	chr12:123612200-123615800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:123612600-123615400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links