Variant report

Variant	rs12298398
Chromosome Location	chr12:61207768-61207769
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10082833	0.93[EUR][1000 genomes]
rs1032641	0.93[EUR][1000 genomes]
rs1032642	0.93[EUR][1000 genomes]
rs1032643	0.94[EUR][1000 genomes]
rs1032644	0.93[EUR][1000 genomes]
rs10747882	0.81[EUR][1000 genomes]
rs10784067	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784068	0.96[EUR][1000 genomes]
rs10877452	0.92[EUR][1000 genomes]
rs10877453	0.91[EUR][1000 genomes]
rs10877458	0.92[EUR][1000 genomes]
rs11173581	0.87[EUR][1000 genomes]
rs11173622	0.91[EUR][1000 genomes]
rs11173624	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173625	0.93[EUR][1000 genomes]
rs11173626	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11173627	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173628	0.94[EUR][1000 genomes]
rs11173630	0.94[EUR][1000 genomes]
rs11173634	0.94[EUR][1000 genomes]
rs11173653	0.87[EUR][1000 genomes]
rs12296489	0.89[EUR][1000 genomes]
rs12296661	0.93[EUR][1000 genomes]
rs12301122	0.93[EUR][1000 genomes]
rs12320516	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12321112	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353732	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1587345	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1604715	0.85[EUR][1000 genomes]
rs2654655	0.85[EUR][1000 genomes]
rs273780	0.86[EUR][1000 genomes]
rs273781	0.83[EUR][1000 genomes]
rs273782	0.85[EUR][1000 genomes]
rs273785	0.85[EUR][1000 genomes]
rs273787	0.86[EUR][1000 genomes]
rs4758883	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61040712	0.92[EUR][1000 genomes]
rs6581347	0.93[EUR][1000 genomes]
rs6581348	0.92[EUR][1000 genomes]
rs7134059	0.93[EUR][1000 genomes]
rs7301607	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73382964	0.94[EUR][1000 genomes]
rs7485220	0.93[EUR][1000 genomes]
rs7486370	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486659	0.87[EUR][1000 genomes]
rs7487354	0.93[EUR][1000 genomes]
rs7488590	0.96[EUR][1000 genomes]
rs7488790	0.92[EUR][1000 genomes]
rs7953872	0.93[EUR][1000 genomes]
rs9669114	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9919781	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047466	chr12:60702221-61521156	Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv899139	chr12:61043705-61316609	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv559144	chr12:61054803-61214545	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv826400	chr12:61086823-61240180	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1067599	chr12:61091958-61921447	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv492252	chr12:61091958-61921447	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1045192	chr12:61099246-61941879	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv559145	chr12:61103562-61315791	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv899140	chr12:61105785-61316609	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv832433	chr12:61110494-61297319	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv559146	chr12:61119266-61315791	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv899141	chr12:61119266-61316609	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv526849	chr12:61154009-61253485	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv559147	chr12:61154009-61315791	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv559148	chr12:61161511-61258329	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv983506	chr12:61196825-61207927	ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12298398	DNAJC14	cis	cerebellum	SCAN
rs12298398	R3HDM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:61206400-61213000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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