Variant report

Variant	rs11689339
Chromosome Location	chr2:72875709-72875710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10180259	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496184	0.85[CEU][hapmap]
rs10496185	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs10496187	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11126369	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs11126378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11126382	0.85[AFR][1000 genomes]
rs11126386	0.85[AFR][1000 genomes]
rs11675268	0.84[CEU][hapmap]
rs11689707	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs11884162	0.85[CEU][hapmap]
rs11884266	0.92[CEU][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11892598	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12619068	0.88[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs12619565	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1562361	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008186	0.85[CEU][hapmap]
rs17008208	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs17008241	1.00[CEU][hapmap]
rs17008293	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs17008315	0.92[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17008360	0.85[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008369	0.85[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008371	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17263172	0.85[CEU][hapmap]
rs1876488	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1949377	0.85[CEU][hapmap]
rs2068410	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4597553	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4852292	0.82[YRI][hapmap]
rs55642420	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058174	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57192957	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58890506	0.86[AFR][1000 genomes]
rs59216875	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60284189	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60314340	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61619102	0.86[AFR][1000 genomes]
rs61736520	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6546777	0.85[YRI][hapmap]
rs66469454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509842	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66794803	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713143	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6716335	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6720889	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs6736649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739768	1.00[CEU][hapmap]
rs6740390	1.00[CEU][hapmap]
rs6749495	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6754072	1.00[ASN][1000 genomes]
rs6756070	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs6761253	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs67869181	0.93[EUR][1000 genomes]
rs67926386	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67927720	0.82[AFR][1000 genomes]
rs7557942	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7565198	0.85[YRI][hapmap]
rs7577244	0.85[CEU][hapmap]
rs7591025	0.85[YRI][hapmap]
rs7593084	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7604083	1.00[CEU][hapmap]
rs7604818	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7607226	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs764766	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11689339	TGFA	cis	cerebellum	SCAN
rs11689339	AUP1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72840200-72878600	Weak transcription	Aorta	Aorta
2	chr2:72858400-72904000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:72866200-72877400	Weak transcription	Fetal Heart	heart
4	chr2:72866800-72902600	Weak transcription	Left Ventricle	heart
5	chr2:72873000-72903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:72875000-72877400	Weak transcription	Brain Substantia Nigra	brain
7	chr2:72875200-72876200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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