Variant report

Variant	rs10492821
Chromosome Location	chr16:72470824-72470825
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1006805	0.81[EUR][1000 genomes]
rs10153187	0.81[ASN][1000 genomes]
rs10468266	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10492822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643203	0.93[AMR][1000 genomes]
rs12051542	0.81[EUR][1000 genomes]
rs12325146	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12325151	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12599375	0.80[EUR][1000 genomes]
rs12708933	0.91[CEU][hapmap]
rs1297137	0.87[ASN][1000 genomes]
rs13333122	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1429071	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1429072	0.80[EUR][1000 genomes]
rs16970933	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971030	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16971035	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16971036	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16971037	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16971050	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16971112	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes]
rs17287903	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17359949	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17608394	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17608557	0.91[CEU][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17609544	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17609577	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17609787	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17609808	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17669912	0.84[ASN][1000 genomes]
rs17676691	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17676709	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17677146	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677484	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17677616	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17677890	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864229	0.84[EUR][1000 genomes]
rs2163068	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2262554	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2336437	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905697	0.80[EUR][1000 genomes]
rs2905699	0.83[EUR][1000 genomes]
rs2914774	0.80[EUR][1000 genomes]
rs2914779	0.82[EUR][1000 genomes]
rs2967232	0.83[EUR][1000 genomes]
rs2967234	0.91[CEU][hapmap]
rs55766519	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55808336	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56323671	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56347149	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56348767	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56389222	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57220817	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57755001	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58549165	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58745414	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58770834	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58860566	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59966262	0.90[ASN][1000 genomes]
rs60502114	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60731174	0.82[ASN][1000 genomes]
rs60855478	0.88[ASN][1000 genomes]
rs61475520	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051129	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62051130	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62051131	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62051136	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62051137	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62051145	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62051146	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62051147	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62051148	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051149	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62051150	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62051151	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62051486	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62051488	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62052871	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62052877	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62052878	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62052879	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62052881	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62052888	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052890	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052891	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052894	0.91[ASN][1000 genomes]
rs62052895	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62052909	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052911	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052915	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62052920	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62052921	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62052923	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62052927	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62052954	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62053968	0.84[ASN][1000 genomes]
rs62053991	0.88[ASN][1000 genomes]
rs62053995	0.87[ASN][1000 genomes]
rs62053996	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62053997	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62053998	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62054469	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62054470	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7192221	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7193177	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7194024	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195825	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198449	0.88[ASN][1000 genomes]
rs7198788	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7199954	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199970	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7200367	0.81[ASN][1000 genomes]
rs7200814	0.88[ASN][1000 genomes]
rs7204260	0.86[ASN][1000 genomes]
rs7205109	0.91[CEU][hapmap];1.00[GIH][hapmap]
rs7205716	0.87[ASN][1000 genomes]
rs7206298	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72791149	0.90[ASN][1000 genomes]
rs72793244	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72793252	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72793263	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72793266	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72793271	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8046749	0.80[EUR][1000 genomes]
rs8049577	0.82[EUR][1000 genomes]
rs8050815	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8056067	0.84[ASN][1000 genomes]
rs8058832	0.84[ASN][1000 genomes]
rs8063172	0.84[ASN][1000 genomes]
rs806732	1.00[CHB][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs806733	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs806738	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs806747	0.87[ASN][1000 genomes]
rs9630625	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9922217	0.80[EUR][1000 genomes]
rs999697	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs999698	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1063172	chr16:72342110-72537808	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv542947	chr16:72342110-72537808	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1057127	chr16:72375524-72509686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv542949	chr16:72375524-72509686	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv572956	chr16:72426448-72517014	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv523524	chr16:72464460-72635674	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10492821	PRMT7	cis	cerebellum	SCAN
rs10492821	DHODH	cis	cerebellum	SCAN
rs10492821	THAP11	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72460000-72471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:72470000-72474200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr16:72470400-72471000	Weak transcription	Fetal Brain Female	brain
4	chr16:72470800-72471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr16:72470800-72474400	Weak transcription	Primary B cells from cord blood	blood

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