Variant report

Variant	rs3794320
Chromosome Location	chr12:21444435-21444436
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21442280..21445032-chr12:21445286..21448697,3	K562	blood:

Extended variants
information (count: 158 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1002552	1.00[ASN][1000 genomes]
rs10444413	1.00[ASN][1000 genomes]
rs10770795	0.83[EUR][1000 genomes]
rs10841761	1.00[ASN][1000 genomes]
rs10841766	1.00[ASN][1000 genomes]
rs10841767	1.00[ASN][1000 genomes]
rs10841768	1.00[ASN][1000 genomes]
rs10841784	1.00[ASN][1000 genomes]
rs10841789	1.00[ASN][1000 genomes]
rs10841795	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045771	1.00[ASN][1000 genomes]
rs11045772	1.00[ASN][1000 genomes]
rs11045773	1.00[ASN][1000 genomes]
rs11045780	1.00[ASN][1000 genomes]
rs11045781	1.00[ASN][1000 genomes]
rs11045783	1.00[ASN][1000 genomes]
rs11045785	1.00[ASN][1000 genomes]
rs11045786	1.00[ASN][1000 genomes]
rs11045787	1.00[ASN][1000 genomes]
rs11045796	1.00[ASN][1000 genomes]
rs11045797	1.00[ASN][1000 genomes]
rs11045798	1.00[ASN][1000 genomes]
rs11045799	1.00[ASN][1000 genomes]
rs11045801	1.00[ASN][1000 genomes]
rs11045803	1.00[ASN][1000 genomes]
rs11045805	1.00[ASN][1000 genomes]
rs11045806	1.00[ASN][1000 genomes]
rs11045807	1.00[ASN][1000 genomes]
rs11045813	1.00[ASN][1000 genomes]
rs11045816	1.00[ASN][1000 genomes]
rs11045818	1.00[ASN][1000 genomes]
rs11045819	1.00[ASN][1000 genomes]
rs11045820	1.00[ASN][1000 genomes]
rs11045821	1.00[ASN][1000 genomes]
rs11045823	1.00[ASN][1000 genomes]
rs11045824	1.00[ASN][1000 genomes]
rs11045825	1.00[ASN][1000 genomes]
rs11045831	1.00[ASN][1000 genomes]
rs11045832	1.00[ASN][1000 genomes]
rs11045843	1.00[ASN][1000 genomes]
rs11045856	1.00[ASN][1000 genomes]
rs11045858	1.00[ASN][1000 genomes]
rs11045862	1.00[ASN][1000 genomes]
rs11045863	1.00[ASN][1000 genomes]
rs11045870	1.00[ASN][1000 genomes]
rs11045871	1.00[ASN][1000 genomes]
rs11045872	1.00[ASN][1000 genomes]
rs11045873	1.00[ASN][1000 genomes]
rs11045874	1.00[ASN][1000 genomes]
rs11045884	1.00[ASN][1000 genomes]
rs11045887	1.00[ASN][1000 genomes]
rs11045891	1.00[ASN][1000 genomes]
rs11045892	1.00[ASN][1000 genomes]
rs11045893	1.00[ASN][1000 genomes]
rs11045897	1.00[ASN][1000 genomes]
rs11045916	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045917	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045918	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045928	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045930	1.00[ASN][1000 genomes]
rs11045942	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045946	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045950	0.99[EUR][1000 genomes]
rs11045952	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045953	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045956	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045957	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045958	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045960	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045961	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045962	0.81[EUR][1000 genomes]
rs11045972	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045978	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045981	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11494720	1.00[ASN][1000 genomes]
rs11513226	1.00[ASN][1000 genomes]
rs11513228	1.00[ASN][1000 genomes]
rs11513411	1.00[ASN][1000 genomes]
rs11522782	1.00[ASN][1000 genomes]
rs12307908	1.00[ASN][1000 genomes]
rs12311451	1.00[ASN][1000 genomes]
rs12367829	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368356	1.00[ASN][1000 genomes]
rs12368481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370842	1.00[ASN][1000 genomes]
rs12371160	1.00[ASN][1000 genomes]
rs12371570	1.00[ASN][1000 genomes]
rs12371691	1.00[ASN][1000 genomes]
rs12372124	1.00[ASN][1000 genomes]
rs12812279	1.00[ASN][1000 genomes]
rs12814646	1.00[ASN][1000 genomes]
rs12815795	1.00[ASN][1000 genomes]
rs12819994	1.00[ASN][1000 genomes]
rs12820529	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821068	1.00[ASN][1000 genomes]
rs12821228	1.00[ASN][1000 genomes]
rs12821721	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829704	1.00[ASN][1000 genomes]
rs12830545	1.00[ASN][1000 genomes]
rs1564367	1.00[ASN][1000 genomes]
rs1564369	1.00[ASN][1000 genomes]
rs17328763	1.00[ASN][1000 genomes]
rs17329885	1.00[ASN][1000 genomes]
rs2169969	1.00[ASN][1000 genomes]
rs2199684	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2199686	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417972	1.00[ASN][1000 genomes]
rs28802276	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34022980	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34111581	1.00[ASN][1000 genomes]
rs34211424	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34249976	1.00[ASN][1000 genomes]
rs34632551	1.00[ASN][1000 genomes]
rs34888642	1.00[ASN][1000 genomes]
rs35157563	1.00[ASN][1000 genomes]
rs35236625	1.00[ASN][1000 genomes]
rs35406304	1.00[ASN][1000 genomes]
rs35462387	1.00[ASN][1000 genomes]
rs35642680	1.00[ASN][1000 genomes]
rs35736956	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901590	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35928112	1.00[ASN][1000 genomes]
rs3794319	0.81[EUR][1000 genomes]
rs4149002	0.81[EUR][1000 genomes]
rs4149006	0.81[EUR][1000 genomes]
rs4337089	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381410	1.00[ASN][1000 genomes]
rs4442593	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55720923	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55773124	1.00[ASN][1000 genomes]
rs55820200	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56164184	1.00[ASN][1000 genomes]
rs6487215	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66777941	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137060	1.00[ASN][1000 genomes]
rs71446755	1.00[ASN][1000 genomes]
rs71446757	1.00[ASN][1000 genomes]
rs71446760	1.00[ASN][1000 genomes]
rs71446761	1.00[ASN][1000 genomes]
rs71446762	1.00[ASN][1000 genomes]
rs71446763	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485550	1.00[ASN][1000 genomes]
rs7957274	1.00[ASN][1000 genomes]
rs7960384	1.00[ASN][1000 genomes]
rs7960688	1.00[ASN][1000 genomes]
rs7962263	1.00[ASN][1000 genomes]
rs7962919	1.00[ASN][1000 genomes]
rs7965059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967303	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967403	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977197	1.00[ASN][1000 genomes]
rs7978322	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898883	chr12:21294293-21450917	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv898886	chr12:21354494-21450250	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv898891	chr12:21422253-21453355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv898892	chr12:21428371-21453355	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv557735	chr12:21443282-21538957	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3794320	LST-3TM12	cis	cerebellum	SCAN
rs3794320	GOLT1B	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21411000-21460400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:21416200-21449600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:21416200-21473600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:21422600-21447200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:21426600-21460400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:21440600-21448200	Weak transcription	Brain Angular Gyrus	brain
7	chr12:21441600-21446800	Weak transcription	Brain Substantia Nigra	brain
8	chr12:21442200-21445000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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