Variant report

Variant	rs1491584
Chromosome Location	chr2:114003904-114003905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13015478	0.82[CEU][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13429413	0.87[ASN][1000 genomes]
rs1374161	0.81[JPT][hapmap]
rs1466018	0.87[JPT][hapmap]
rs1491585	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1491586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018348	0.87[CEU][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2863244	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35129549	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762497	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4849187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542127	0.87[JPT][hapmap]
rs6734610	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7560701	0.87[JPT][hapmap]

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	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs1491584	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs1491584	PAX8	cis	Artery Tibial	GTEx
rs1491584	PAX8	cis	multi-tissue	Pritchard
rs1491584	PAX8	cis	lung	GTEx
rs1491584	PAX8	cis	Nerve Tibial	GTEx
rs1491584	AC016683.6	cis	Muscle Skeletal	GTEx
rs1491584	LOC654433	cis	parietal	SCAN
rs1491584	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs1491584	PAX8	cis	Whole Blood	GTEx
rs1491584	AC016683.6	cis	Whole Blood	GTEx
rs1491584	PAX8	cis	Lymphoblastoid	GTEx
rs1491584	AC016683.6	cis	Nerve Tibial	GTEx
rs1491584	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1491584	PAX8	cis	Esophagus Mucosa	GTEx
rs1491584	AC016683.6	cis	Artery Tibial	GTEx
rs1491584	LOC654433	cis	cerebellum	SCAN
rs1491584	PAX8	cis	Adipose Subcutaneous	GTEx
rs1491584	PAX8	cis	lymphoblastoid	seeQTL
rs1491584	AC016683.6	cis	Esophagus Muscularis	GTEx
rs1491584	AC016683.6	cis	lung	GTEx
rs1491584	AC016683.6	cis	Esophagus Mucosa	GTEx
rs1491584	PAX8	cis	Esophagus Muscularis	GTEx
rs1491584	PAX8	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
7	chr2:113998200-114006600	Weak transcription	Fetal Thymus	thymus
8	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:113999200-114005200	Weak transcription	Gastric	stomach
11	chr2:113999200-114007000	Weak transcription	Right Atrium	heart
12	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
14	chr2:113999400-114006600	Weak transcription	Colonic Mucosa	Colon
15	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:113999600-114006600	Weak transcription	K562	blood
17	chr2:113999600-114007000	Weak transcription	HSMMtube	muscle
18	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
20	chr2:113999600-114028400	Weak transcription	Ovary	ovary
21	chr2:113999800-114005200	Weak transcription	Lung	lung
22	chr2:113999800-114006800	Weak transcription	NHLF	lung
23	chr2:114000000-114006600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:114000000-114007000	Weak transcription	HSMM	muscle
25	chr2:114000200-114006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:114000200-114009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
28	chr2:114000600-114006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
30	chr2:114001000-114004000	Enhancers	Fetal Intestine Large	intestine
31	chr2:114001600-114004800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:114002000-114004200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:114002000-114006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:114002000-114006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:114002200-114004000	Enhancers	Liver	Liver
36	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:114003000-114004800	Enhancers	NHEK	skin
38	chr2:114003600-114004000	Enhancers	Primary T cells from cord blood	blood
39	chr2:114003600-114004200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:114003600-114004200	Enhancers	HepG2	liver
41	chr2:114003600-114006000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:114003600-114006400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:114003600-114006600	Weak transcription	Adipose Nuclei	Adipose
44	chr2:114003600-114006600	Weak transcription	A549	lung
45	chr2:114003600-114007000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:114003600-114008400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:114003800-114004800	Strong transcription	Fetal Kidney	kidney
48	chr2:114003800-114006600	Weak transcription	Fetal Intestine Small	intestine
49	chr2:114003800-114006600	Weak transcription	Fetal Muscle Leg	muscle

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