Variant report

Variant	rs17770503
Chromosome Location	chr3:98952443-98952444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1066358	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066359	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066360	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066361	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066362	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066364	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066365	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1066366	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066367	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1082506	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1082507	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082508	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082509	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082510	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082512	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1092312	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11720946	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12053880	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1520680	0.91[EUR][1000 genomes]
rs1608598	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770521	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818726	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1818727	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681447	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2682410	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2687667	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4928154	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58807394	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59080898	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67357616	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67639354	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68096327	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73147953	0.83[EUR][1000 genomes]
rs73147986	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73149623	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs774972	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9968233	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997372	chr3:98864056-98953749	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1008663	chr3:98867385-98953749	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1014277	chr3:98877662-98953749	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004810	chr3:98888976-98953749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1010512	chr3:98893510-98953749	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1012359	chr3:98893510-98965013	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv1798220	chr3:98894142-99020463	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1010851	chr3:98897698-98953749	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1011609	chr3:98924050-98953749	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv998405	chr3:98929420-98952443	Enhancers Flanking Active TSS Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1008312	chr3:98929420-98953749	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv508230	chr3:98933987-98969536	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv2763763	chr3:98937784-98953761	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
18	nsv1012332	chr3:98944446-98969737	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1013972	chr3:98944446-98998206	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv999173	chr3:98944446-99007686	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1002786	chr3:98944446-99013936	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1014178	chr3:98945194-98965013	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17770503	ST3GAL6	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98951400-98952800	Enhancers	Osteobl	bone
2	chr3:98952200-98959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:98952200-98959200	Weak transcription	Muscle Satellite Cultured Cells	--

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