Variant report

Variant	rs12990456
Chromosome Location	chr2:114011914-114011915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11123173	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001920	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13429413	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466018	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491585	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2863244	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4142815	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849188	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6542127	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6726151	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6734610	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7560701	0.88[ASN][1000 genomes]
rs895418	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12990456	AC016683.6	cis	Whole Blood	GTEx
rs12990456	AC016683.6	cis	Muscle Skeletal	GTEx
rs12990456	AC016683.6	cis	Artery Tibial	GTEx
rs12990456	AC016683.6	cis	Esophagus Mucosa	GTEx
rs12990456	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs12990456	PAX8	cis	Esophagus Mucosa	GTEx
rs12990456	AC016683.6	cis	lung	GTEx
rs12990456	PAX8	cis	Esophagus Muscularis	GTEx
rs12990456	PAX8	cis	Adipose Subcutaneous	GTEx
rs12990456	LOC654433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
4	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
6	chr2:113999600-114028400	Weak transcription	Ovary	ovary
7	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
8	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:114006600-114012200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:114006600-114016200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:114006600-114016200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:114006800-114015800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:114007200-114014800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:114007200-114016800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:114008000-114012000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:114008000-114013200	Weak transcription	HSMMtube	muscle
17	chr2:114008400-114012600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:114008400-114012800	Enhancers	Fetal Thymus	thymus
19	chr2:114008400-114016000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:114008600-114012400	Weak transcription	A549	lung
21	chr2:114008800-114013200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:114009000-114013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:114009000-114013000	Weak transcription	NH-A	brain
24	chr2:114009000-114013800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:114009000-114015000	Weak transcription	K562	blood
26	chr2:114009000-114015400	Weak transcription	Left Ventricle	heart
27	chr2:114009200-114014400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:114009200-114015400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:114009800-114014000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:114009800-114019000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:114010000-114013000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:114010000-114016200	Enhancers	Primary T cells from cord blood	blood
33	chr2:114010000-114016200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:114010200-114012000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:114010200-114013000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:114010200-114013000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:114010200-114013000	Weak transcription	Lung	lung
38	chr2:114010200-114013800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:114010200-114014800	Weak transcription	Adipose Nuclei	Adipose
40	chr2:114010200-114014800	Weak transcription	Fetal Heart	heart
41	chr2:114010200-114014800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:114010200-114015000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:114010200-114015400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr2:114010200-114015800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
46	chr2:114010400-114012200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:114010400-114012200	Enhancers	NHEK	skin
48	chr2:114010400-114022400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:114010600-114012200	Strong transcription	Fetal Kidney	kidney
50	chr2:114010600-114012400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links