Variant report

Variant	rs13016079
Chromosome Location	chr2:52573705-52573706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12991278	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999799	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999852	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005607	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006867	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012043	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13013842	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013911	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017636	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018183	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13019134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020890	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033584	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417515	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1364575	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364583	1.00[ASN][1000 genomes]
rs1424802	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222686	1.00[ASN][1000 genomes]
rs34219622	1.00[ASN][1000 genomes]
rs34793475	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34868438	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35054050	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35695189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35721673	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35872223	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522646	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971594	1.00[ASN][1000 genomes]
rs4971595	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55648425	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55855257	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55962941	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56314551	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333115	1.00[ASN][1000 genomes]
rs56383411	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56390006	1.00[ASN][1000 genomes]
rs71411584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411585	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411587	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411588	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411589	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941055	1.00[ASN][1000 genomes]
rs941056	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941057	0.88[EUR][1000 genomes];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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv834025	chr2:52514959-52693049	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv874113	chr2:52521126-52609707	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv874114	chr2:52521126-52628235	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv998227	chr2:52527889-52821980	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv874115	chr2:52553023-52609707	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv581928	chr2:52572167-52656594	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52565000-52577800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:52567400-52583600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:52571200-52579800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:52573000-52579800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:52573200-52583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:52573400-52574400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:52573600-52578800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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