Variant report

Variant	rs10482689
Chromosome Location	chr5:142675823-142675824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10042945	1.00[JPT][hapmap]
rs10051482	1.00[JPT][hapmap]
rs10052957	0.81[GIH][hapmap]
rs10076665	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10482605	0.83[AMR][1000 genomes]
rs10482633	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10482642	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10482679	1.00[CHD][hapmap]
rs10482682	1.00[ASW][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs10482700	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515521	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740747	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740792	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1438731	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17287758	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17339831	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1837262	0.80[GIH][hapmap]
rs1866388	0.81[GIH][hapmap]
rs258750	0.81[GIH][hapmap]
rs258813	0.82[GIH][hapmap]
rs2918416	0.81[GIH][hapmap]
rs2918417	0.81[GIH][hapmap]
rs2963149	0.81[GIH][hapmap]
rs4128428	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6188	0.81[GIH][hapmap]
rs6198	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72801052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72801070	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72801079	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801081	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801083	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801086	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72801088	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7723528	1.00[JPT][hapmap]
rs852977	0.85[GIH][hapmap]
rs852982	0.85[GIH][hapmap]
rs860457	0.85[GIH][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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv5041	chr5:142653189-142697896	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10482689	NR3C1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
2	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
3	chr5:142655800-142699200	Strong transcription	Dnd41	blood
4	chr5:142656000-142677400	Weak transcription	Gastric	stomach
5	chr5:142656600-142677000	Weak transcription	Lung	lung
6	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
7	chr5:142658000-142679000	Weak transcription	Colonic Mucosa	Colon
8	chr5:142658200-142694800	Weak transcription	Right Ventricle	heart
9	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
10	chr5:142658800-142677400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:142659400-142677200	Weak transcription	HSMMtube	muscle
12	chr5:142659600-142677400	Weak transcription	Ovary	ovary
13	chr5:142659800-142679400	Weak transcription	Small Intestine	intestine
14	chr5:142659800-142692600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:142661600-142677200	Weak transcription	HUVEC	blood vessel
16	chr5:142664000-142677400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:142664000-142684600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:142664000-142685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:142664400-142681200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:142664400-142693400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:142667200-142682000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:142667400-142688800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr5:142667800-142681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:142668000-142680200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:142668200-142680200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:142668600-142678400	Strong transcription	A549	lung
27	chr5:142668600-142680400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:142668600-142680800	Strong transcription	NHDF-Ad	bronchial
29	chr5:142668600-142688800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:142668800-142676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:142668800-142678600	Weak transcription	Fetal Stomach	stomach
32	chr5:142668800-142682400	Strong transcription	GM12878-XiMat	blood
33	chr5:142668800-142693800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:142669000-142680800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:142669200-142680200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:142669400-142680400	Strong transcription	Osteobl	bone
37	chr5:142669600-142682600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr5:142669800-142677200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:142669800-142680200	Strong transcription	Primary T cells from cord blood	blood
40	chr5:142669800-142680200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr5:142669800-142680400	Strong transcription	Fetal Muscle Leg	muscle
42	chr5:142669800-142680400	Strong transcription	Fetal Thymus	thymus
43	chr5:142669800-142680400	Strong transcription	Thymus	Thymus
44	chr5:142669800-142680600	Strong transcription	Adipose Nuclei	Adipose
45	chr5:142669800-142681200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:142670000-142676600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr5:142670000-142680200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:142670000-142681800	Strong transcription	Primary B cells from cord blood	blood
49	chr5:142670000-142683600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:142670200-142680400	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links