Variant report

Variant	rs4417749
Chromosome Location	chr2:189991765-189991766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10165127	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10165257	0.89[EUR][1000 genomes]
rs1016622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11901914	0.92[EUR][1000 genomes]
rs12618316	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005714	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005834	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006065	0.89[EUR][1000 genomes]
rs13013089	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019651	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13020999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024858	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]
rs13030984	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031211	0.81[LWK][hapmap]
rs1356164	0.82[YRI][hapmap]
rs1356168	0.81[LWK][hapmap]
rs1464135	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1515864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515869	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533618	0.85[EUR][1000 genomes]
rs1949327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965422	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2138373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138374	0.85[YRI][hapmap]
rs36019389	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428040	0.82[AFR][1000 genomes]
rs4667263	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667264	0.81[LWK][hapmap]
rs4667265	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs4667266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4667271	0.85[EUR][1000 genomes]
rs4998559	0.82[YRI][hapmap]
rs62182417	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708419	0.85[YRI][hapmap]
rs6730236	0.92[CHB][hapmap]
rs6741804	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561002	0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs7593860	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599222	0.85[EUR][1000 genomes]
rs7606337	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[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
rs4417749	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 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	chr2:189981000-189993400	Weak transcription	Ovary	ovary
5	chr2:189981200-189992800	Weak transcription	NH-A	brain
6	chr2:189981200-189998000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:189981400-189991800	Weak transcription	HSMMtube	muscle
8	chr2:189981400-189992800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
10	chr2:189982400-190005800	Weak transcription	Fetal Kidney	kidney
11	chr2:189982600-189992600	Weak transcription	NHLF	lung
12	chr2:189983400-189992000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:189984200-189992600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:189985400-190000200	Weak transcription	Fetal Lung	lung
16	chr2:189985600-189992600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:189986000-190008800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:189986400-189992000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:189988400-189993400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:189989000-189991800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:189990400-189992600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:189991200-189992800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:189991400-189991800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:189991400-189992600	Genic enhancers	NHDF-Ad	bronchial
25	chr2:189991400-189992800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:189991400-189993000	Genic enhancers	Osteobl	bone
27	chr2:189991400-189993200	Enhancers	Colon Smooth Muscle	Colon
28	chr2:189991400-189993200	Genic enhancers	HSMM	muscle
29	chr2:189991600-189992000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:189991600-189992200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:189991600-189992800	Weak transcription	A549	lung
32	chr2:189991600-189993200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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