Variant report

Variant	rs10841781
Chromosome Location	chr12:21419395-21419396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 158 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10431251	0.95[ASN][1000 genomes]
rs10459074	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10459075	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10743411	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10743412	0.87[ASN][1000 genomes]
rs10770795	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770796	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10770797	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10841777	0.98[ASN][1000 genomes]
rs10841778	0.96[ASN][1000 genomes]
rs10841779	0.98[ASN][1000 genomes]
rs10841780	0.98[ASN][1000 genomes]
rs10841782	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10841786	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10841787	0.97[ASN][1000 genomes]
rs10841790	0.85[ASN][1000 genomes]
rs10841791	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10841794	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10841795	0.91[CEU][hapmap]
rs11045916	0.91[CEU][hapmap]
rs11045918	0.83[CEU][hapmap]
rs11045922	0.94[ASN][1000 genomes]
rs11045923	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs11045924	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[ASN][1000 genomes]
rs11045925	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs11045929	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs11045941	0.96[ASN][1000 genomes]
rs11045942	0.91[CEU][hapmap]
rs11045944	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11045946	0.91[CEU][hapmap]
rs11045948	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11045952	0.91[CEU][hapmap]
rs11045953	0.91[CEU][hapmap]
rs11045954	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11045955	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11045956	0.91[CEU][hapmap]
rs11045957	0.91[CEU][hapmap]
rs11045958	0.91[CEU][hapmap]
rs11045960	0.91[CEU][hapmap]
rs11045961	0.91[CEU][hapmap]
rs11045962	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11045965	0.86[ASN][1000 genomes]
rs11045966	0.82[ASN][1000 genomes]
rs11045967	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045968	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045969	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11045970	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045971	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045972	0.91[CEU][hapmap]
rs11045974	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045975	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs11045976	0.87[ASN][1000 genomes]
rs11045978	0.90[CEU][hapmap]
rs11045980	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11533477	0.95[ASN][1000 genomes]
rs11535998	0.96[ASN][1000 genomes]
rs11536000	0.95[ASN][1000 genomes]
rs11537394	0.95[ASN][1000 genomes]
rs11561152	0.96[ASN][1000 genomes]
rs12227319	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12228765	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12230113	0.96[ASN][1000 genomes]
rs12230401	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12231212	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12231484	0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs12231738	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs12311809	0.93[ASN][1000 genomes]
rs12581287	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12581327	0.98[ASN][1000 genomes]
rs16923597	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2127117	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2127118	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2169883	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2199684	0.91[CEU][hapmap]
rs2199686	0.91[CEU][hapmap]
rs2219791	0.87[ASN][1000 genomes]
rs2219793	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306226	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306227	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306229	0.85[ASN][1000 genomes]
rs2306231	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2417971	0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2417974	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2900480	0.91[CEU][hapmap]
rs36089711	0.95[ASN][1000 genomes]
rs3736080	0.95[ASN][1000 genomes]
rs3736081	0.95[ASN][1000 genomes]
rs3751270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764041	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764042	0.87[ASN][1000 genomes]
rs3764044	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.95[ASN][1000 genomes]
rs3764045	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs3794319	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4115170	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4140389	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4148977	0.87[ASN][1000 genomes]
rs4148978	0.87[ASN][1000 genomes]
rs4148981	0.88[ASN][1000 genomes]
rs4148982	0.87[ASN][1000 genomes]
rs4148983	0.87[ASN][1000 genomes]
rs4148984	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148985	0.87[ASN][1000 genomes]
rs4148986	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148987	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148988	0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148989	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148990	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148991	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148992	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4148993	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4148994	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4148995	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4148996	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4148997	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4148998	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148999	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4149001	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4149002	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149003	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4149004	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4149005	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[ASN][1000 genomes]
rs4149006	0.85[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4149007	0.95[ASN][1000 genomes]
rs4149008	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4149009	0.95[ASN][1000 genomes]
rs4337089	0.91[CEU][hapmap]
rs57899519	0.94[ASN][1000 genomes]
rs6487215	0.91[CEU][hapmap]
rs6487216	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6487217	0.87[ASN][1000 genomes]
rs7296472	0.87[ASN][1000 genomes]
rs7300346	0.87[ASN][1000 genomes]
rs7300463	0.87[ASN][1000 genomes]
rs7305911	0.92[ASN][1000 genomes]
rs7313671	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs7315667	0.87[ASN][1000 genomes]
rs7955581	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7957203	0.87[ASN][1000 genomes]
rs7963398	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7967303	0.91[CEU][hapmap]
rs7967354	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7967403	0.91[CEU][hapmap]
rs7967935	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7968331	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7968842	0.87[ASN][1000 genomes]
rs7977517	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7977652	0.88[ASN][1000 genomes]
rs7978322	0.91[CEU][hapmap]
rs7978981	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7980842	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs875234	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948700	chr12:21008498-21422492	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv515735	chr12:21010048-21420712	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1052587	chr12:21149131-21420712	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1050396	chr12:21152478-21420712	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv898888	chr12:21355537-21426087	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10841781	LST-3TM12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21411000-21460400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:21415800-21420000	Weak transcription	Liver	Liver
3	chr12:21416200-21449600	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:21416200-21473600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:21417000-21429800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:21417200-21425800	Weak transcription	Brain Anterior Caudate	brain
7	chr12:21418200-21421200	Enhancers	Primary monocytes fromperipheralblood	blood

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