Variant report

Variant	rs13417515
Chromosome Location	chr2:52503364-52503365
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12991278	1.00[ASN][1000 genomes]
rs12999799	1.00[ASN][1000 genomes]
rs12999852	1.00[ASN][1000 genomes]
rs13005607	1.00[ASN][1000 genomes]
rs13006867	1.00[ASN][1000 genomes]
rs13012043	1.00[ASN][1000 genomes]
rs13013842	1.00[ASN][1000 genomes]
rs13013911	1.00[ASN][1000 genomes]
rs13016079	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13017636	1.00[ASN][1000 genomes]
rs13018183	1.00[ASN][1000 genomes]
rs13019134	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13020890	1.00[ASN][1000 genomes]
rs13033584	1.00[ASN][1000 genomes]
rs1364575	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1364583	1.00[ASN][1000 genomes]
rs1424802	1.00[ASN][1000 genomes]
rs2222686	1.00[ASN][1000 genomes]
rs34219622	1.00[ASN][1000 genomes]
rs34793475	1.00[ASN][1000 genomes]
rs34868438	1.00[ASN][1000 genomes]
rs35054050	1.00[ASN][1000 genomes]
rs35695189	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35721673	1.00[ASN][1000 genomes]
rs35872223	1.00[ASN][1000 genomes]
rs4522646	1.00[ASN][1000 genomes]
rs4971594	1.00[ASN][1000 genomes]
rs4971595	1.00[ASN][1000 genomes]
rs55648425	1.00[ASN][1000 genomes]
rs55855257	1.00[ASN][1000 genomes]
rs55962941	1.00[ASN][1000 genomes]
rs56144224	0.81[AFR][1000 genomes]
rs56314551	1.00[ASN][1000 genomes]
rs56333115	1.00[ASN][1000 genomes]
rs56383411	1.00[ASN][1000 genomes]
rs56390006	1.00[ASN][1000 genomes]
rs71411584	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71411585	1.00[ASN][1000 genomes]
rs71411587	1.00[ASN][1000 genomes]
rs71411588	1.00[ASN][1000 genomes]
rs71411589	1.00[ASN][1000 genomes]
rs941055	1.00[ASN][1000 genomes]
rs941056	1.00[ASN][1000 genomes]
rs941057	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1007633	chr2:52217555-52862389	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535714	chr2:52217555-52862389	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874100	chr2:52247287-52503364	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv998637	chr2:52370482-52527949	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv874110	chr2:52383698-52582535	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv874111	chr2:52383698-52962055	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1013464	chr2:52398592-52585274	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1011669	chr2:52400144-52585274	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv581927	chr2:52407060-52582766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv997910	chr2:52413474-52584090	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1006897	chr2:52413474-52585274	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2763265	chr2:52413486-52584090	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv874112	chr2:52414723-52549472	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1014046	chr2:52420457-52584090	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv999119	chr2:52439479-52572735	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv535716	chr2:52439479-52572735	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv999967	chr2:52448661-52588775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1014619	chr2:52496317-52821980	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv535717	chr2:52496317-52821980	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv523804	chr2:52503364-52553023	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13417515	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52503200-52504200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:52503200-52504400	Enhancers	HUES6 Cell Line	embryonic stem cell

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