Variant report

Variant	rs1304898
Chromosome Location	chr2:56759963-56759964
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1017268	0.85[ASN][1000 genomes]
rs1017269	0.85[ASN][1000 genomes]
rs1017270	0.86[ASN][1000 genomes]
rs10490407	0.80[ASN][1000 genomes]
rs10490408	0.85[ASN][1000 genomes]
rs10490409	0.85[ASN][1000 genomes]
rs11678015	0.89[ASN][1000 genomes]
rs11685181	0.99[ASN][1000 genomes]
rs12619260	0.88[ASN][1000 genomes]
rs1304897	0.89[ASN][1000 genomes]
rs1304899	0.89[ASN][1000 genomes]
rs13388596	0.96[ASN][1000 genomes]
rs1477521	0.85[ASN][1000 genomes]
rs1477522	0.85[ASN][1000 genomes]
rs17048063	0.86[ASN][1000 genomes]
rs17048064	0.86[ASN][1000 genomes]
rs17048067	0.86[ASN][1000 genomes]
rs17268931	0.84[ASN][1000 genomes]
rs1978531	0.82[ASN][1000 genomes]
rs2033010	0.85[ASN][1000 genomes]
rs2113863	0.85[ASN][1000 genomes]
rs2162025	0.81[ASN][1000 genomes]
rs2194798	0.87[ASN][1000 genomes]
rs2216972	0.85[ASN][1000 genomes]
rs2870064	0.91[AFR][1000 genomes]
rs4672123	0.85[ASN][1000 genomes]
rs4672128	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788501	0.85[ASN][1000 genomes]
rs62161637	0.81[ASN][1000 genomes]
rs6706912	0.89[ASN][1000 genomes]
rs6718973	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735514	0.99[ASN][1000 genomes]
rs67395716	0.85[ASN][1000 genomes]
rs7566356	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7580218	0.88[ASN][1000 genomes]
rs7580549	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592784	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987575	0.88[EUR][1000 genomes]
rs987576	0.85[ASN][1000 genomes]
rs989729	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874172	chr2:56638856-56811749	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757800	chr2:56659685-56851198	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2759052	chr2:56659685-56851198	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2752438	chr2:56700945-56788111	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv874173	chr2:56702495-56761626	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv874174	chr2:56702495-56761998	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv582049	chr2:56702495-56787100	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv582050	chr2:56702495-56854346	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2756921	chr2:56706672-56811290	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv582051	chr2:56706758-56902709	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv874175	chr2:56731966-56821883	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv874176	chr2:56736097-56821883	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv874177	chr2:56739650-56821883	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv874178	chr2:56739650-56839139	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv35146	chr2:56741749-56811290	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv817973	chr2:56743435-56817927	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1005729	chr2:56750209-56778009	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1005547	chr2:56751574-56887287	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1304898	SPTBN1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56758800-56760000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:56758800-56762400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr2:56759000-56762200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:56759600-56761000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:56759800-56760000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr2:56759800-56761200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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