Variant report

Variant	rs17051321
Chromosome Location	chr4:122119449-122119450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10004221	0.81[EUR][1000 genomes]
rs10015340	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10446733	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454795	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518383	0.95[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11098605	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947841	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101385	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102428	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104663	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13104875	0.81[ASN][1000 genomes]
rs13106084	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106137	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107912	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108214	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13108739	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13109100	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112923	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115256	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116723	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116936	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13118027	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118913	0.81[EUR][1000 genomes]
rs13123960	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124511	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124522	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126929	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128962	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13129000	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13129293	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133184	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13133221	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133584	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137539	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138203	0.84[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13143534	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13150702	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13151913	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13152159	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13152687	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511094	0.81[EUR][1000 genomes]
rs17051320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858291	0.90[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2068019	0.81[EUR][1000 genomes]
rs2136942	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2136943	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2198315	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2218959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28513714	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28530598	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35449703	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35971082	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36087391	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817171	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6534254	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812399	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812515	0.84[ASN][1000 genomes]
rs6814480	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820363	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821331	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828327	0.81[EUR][1000 genomes]
rs6833114	0.95[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6835790	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838000	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839386	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839726	0.83[EUR][1000 genomes]
rs6846458	0.95[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6855628	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs6856825	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71629498	0.94[ASN][1000 genomes]
rs7680038	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7684168	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs867883	0.81[EUR][1000 genomes]
rs896621	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9284633	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9307490	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998327	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992960	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9993163	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998339	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879860	chr4:122030864-122126808	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17051321	TNIP3	cis	cerebellum	SCAN
rs17051321	PRDM5	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122113800-122119600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr4:122114000-122119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:122114000-122120600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:122114400-122120400	Weak transcription	Primary T cells from cord blood	blood
5	chr4:122114600-122119800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:122115000-122119600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:122115200-122120400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:122117600-122119600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:122119400-122119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:122119400-122120200	Enhancers	GM12878-XiMat	blood
11	chr4:122119400-122121800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links