Variant report

Variant	rs13024858
Chromosome Location	chr2:189981212-189981213
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165127	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10165257	0.86[EUR][1000 genomes]
rs1016622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11901914	0.89[EUR][1000 genomes]
rs12618316	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13005714	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13005834	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006065	0.86[EUR][1000 genomes]
rs13013089	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13019651	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13020999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030984	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464135	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1515864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515869	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533618	0.82[EUR][1000 genomes]
rs1949327	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36019389	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417749	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667263	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4667271	0.82[EUR][1000 genomes]
rs62182417	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434325	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6730236	0.92[CHB][hapmap]
rs6741804	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6749559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593860	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7599222	0.82[EUR][1000 genomes]
rs7606337	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9288163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13024858	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189962400-189995200	Weak transcription	Aorta	Aorta
2	chr2:189968600-190012000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:189974800-190007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:189975200-189988600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:189975400-189988600	Weak transcription	HUVEC	blood vessel
6	chr2:189976000-189986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:189979200-189984000	Enhancers	Osteobl	bone
8	chr2:189979200-189984200	Enhancers	A549	lung
9	chr2:189979400-189983200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:189980200-189981400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:189980200-189981600	Enhancers	Adipose Nuclei	Adipose
12	chr2:189980200-189982600	Enhancers	Fetal Lung	lung
13	chr2:189980400-189981400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:189980400-189982600	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:189980600-189981400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr2:189980600-189981400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:189980600-189981400	Flanking Active TSS	NHDF-Ad	bronchial
18	chr2:189980600-189982000	Enhancers	Stomach Smooth Muscle	stomach
19	chr2:189980800-189981400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:189980800-189981800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:189981000-189981400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:189981000-189981400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:189981000-189981400	Enhancers	Colon Smooth Muscle	Colon
24	chr2:189981000-189981400	Enhancers	Fetal Stomach	stomach
25	chr2:189981000-189981400	Enhancers	HSMMtube	muscle
26	chr2:189981000-189982600	Enhancers	HSMM	muscle
27	chr2:189981000-189993400	Weak transcription	Ovary	ovary
28	chr2:189981200-189981800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:189981200-189982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:189981200-189982400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:189981200-189982600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:189981200-189982600	Enhancers	NHLF	lung
33	chr2:189981200-189983200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:189981200-189983200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:189981200-189983400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:189981200-189983800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:189981200-189992800	Weak transcription	NH-A	brain
38	chr2:189981200-189998000	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links