Variant report

Variant	rs6438120
Chromosome Location	chr3:112665968-112665969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1016348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1032726	0.82[CEU][hapmap]
rs10934190	0.81[ASN][1000 genomes]
rs10934192	0.83[ASN][1000 genomes]
rs10934193	0.83[ASN][1000 genomes]
rs12494693	0.82[CEU][hapmap]
rs12497951	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13326243	0.83[ASN][1000 genomes]
rs1387023	0.86[CHB][hapmap]
rs1387024	0.87[CHB][hapmap]
rs1392785	0.82[CEU][hapmap]
rs1392786	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466872	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1488193	0.91[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs1500879	0.81[ASN][1000 genomes]
rs1844084	0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs1971986	0.83[ASN][1000 genomes]
rs2087284	1.00[CHB][hapmap]
rs2101440	0.84[ASN][1000 genomes]
rs2171509	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399436	0.83[ASN][1000 genomes]
rs2399443	0.83[ASN][1000 genomes]
rs4103791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4234417	1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs4682120	0.83[ASN][1000 genomes]
rs4682125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682440	0.83[ASN][1000 genomes]
rs4682441	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4682444	0.83[ASN][1000 genomes]
rs4682447	0.91[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs6438118	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438119	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766388	0.83[ASN][1000 genomes]
rs6769091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772799	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6784838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791158	0.83[ASN][1000 genomes]
rs6791672	0.84[ASN][1000 genomes]
rs6808249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355890	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611690	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615462	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615572	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap]
rs7622812	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7622814	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7632218	0.81[ASN][1000 genomes]
rs7646849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652504	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652536	0.83[ASN][1000 genomes]
rs9815606	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819079	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9833991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834840	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847365	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9854885	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865242	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868053	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868839	0.84[ASN][1000 genomes]
rs9870335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870568	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9871985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875551	0.81[ASN][1000 genomes]
rs9877631	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9879005	0.82[AMR][1000 genomes]
rs9879149	0.82[CEU][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs9883255	0.83[ASN][1000 genomes]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438120	ZUFSP	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112661000-112669800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:112661200-112677000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:112662000-112667800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:112663800-112666200	ZNF genes & repeats	Primary T cells from cord blood	blood
5	chr3:112663800-112668800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:112664400-112669400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:112664800-112666200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:112665200-112666600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:112665200-112666800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:112665200-112677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:112665600-112675400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:112665800-112666800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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