Variant report

Variant	rs16970929
Chromosome Location	chr16:72471993-72471994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10492820	0.80[AFR][1000 genomes]
rs11075927	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11075928	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11859210	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11860402	1.00[CEU][hapmap]
rs11860511	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11860913	1.00[AMR][1000 genomes]
rs11861074	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11861672	1.00[AMR][1000 genomes]
rs11866292	1.00[AMR][1000 genomes]
rs12103150	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331987	1.00[AMR][1000 genomes]
rs13332257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13333480	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13336634	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338269	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13338313	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13338662	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1429069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1429070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1557813	1.00[EUR][1000 genomes]
rs16943808	1.00[EUR][1000 genomes]
rs16970828	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970987	0.83[AFR][1000 genomes]
rs16970996	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16971006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16971145	1.00[AMR][1000 genomes]
rs1864230	0.96[AFR][1000 genomes]
rs2017748	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2053234	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2107154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2163066	0.88[AFR][1000 genomes]
rs2189339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2336436	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28393088	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2840012	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28459407	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28464989	1.00[AMR][1000 genomes]
rs28473657	1.00[AMR][1000 genomes]
rs28514442	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28568963	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28569075	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28616025	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28679760	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28706881	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28712432	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828717	1.00[AMR][1000 genomes]
rs28882790	1.00[AMR][1000 genomes]
rs28888757	0.80[AFR][1000 genomes]
rs35917623	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4255793	1.00[AMR][1000 genomes]
rs4624185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4788635	0.81[AFR][1000 genomes]
rs55777547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55806458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57841266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58363387	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58819288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59875457	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61192283	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184224	1.00[AMR][1000 genomes]
rs7185566	0.85[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs7187532	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7187674	0.85[EUR][1000 genomes]
rs7187768	1.00[AMR][1000 genomes]
rs7188632	0.82[AFR][1000 genomes]
rs7192337	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7197250	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7198345	0.85[EUR][1000 genomes]
rs7198450	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7199507	1.00[AMR][1000 genomes]
rs7199594	1.00[AMR][1000 genomes]
rs7200007	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7203819	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs726887	0.80[AFR][1000 genomes]
rs73583171	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73583174	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73583188	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73583198	0.83[AMR][1000 genomes]
rs73585209	1.00[AMR][1000 genomes]
rs73587415	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73599411	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73601423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73601436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8043976	1.00[AMR][1000 genomes]
rs8045319	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045813	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8046375	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8046891	1.00[AMR][1000 genomes]
rs8050489	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051123	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8051420	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051595	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8052117	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8053288	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8053566	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8053837	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059369	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063144	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9302636	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9889208	1.00[AMR][1000 genomes]
rs9921281	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9921921	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9922597	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9922853	1.00[AMR][1000 genomes]
rs9923235	1.00[AMR][1000 genomes]
rs9926141	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926706	1.00[AMR][1000 genomes]
rs9927677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9928119	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9928673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929864	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9930862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9932125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933062	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9934152	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9934365	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9934457	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9935400	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935826	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9937525	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9937973	0.81[AFR][1000 genomes];0.85[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
rs16970929	TMEM155	trans	brain	seeQTL
rs16970929	NELL1	trans	brain	seeQTL
rs16970929	TAC1	trans	brain	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72470000-72474200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr16:72470800-72474400	Weak transcription	Primary B cells from cord blood	blood
3	chr16:72471000-72472600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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