Variant report

Variant	rs16970828
Chromosome Location	chr16:72355139-72355140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10492820	0.87[AFR][1000 genomes]
rs11075927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075928	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11859210	1.00[AMR][1000 genomes]
rs11859361	0.84[EUR][1000 genomes]
rs11860402	1.00[CEU][hapmap]
rs11860511	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11860913	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11861074	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12103150	1.00[AMR][1000 genomes]
rs13330202	0.84[EUR][1000 genomes]
rs13333424	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333480	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336735	0.84[EUR][1000 genomes]
rs13338269	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13338313	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13339625	1.00[AMR][1000 genomes]
rs1429069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1429070	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970746	0.84[EUR][1000 genomes]
rs16970748	0.84[EUR][1000 genomes]
rs16970775	0.84[EUR][1000 genomes]
rs16970782	0.84[EUR][1000 genomes]
rs16970897	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970929	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970996	1.00[AMR][1000 genomes]
rs16971006	1.00[AMR][1000 genomes]
rs1864230	0.81[AFR][1000 genomes]
rs2017748	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053234	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2107154	1.00[AMR][1000 genomes]
rs2189339	1.00[AMR][1000 genomes]
rs2336436	1.00[AMR][1000 genomes]
rs28387686	0.84[EUR][1000 genomes]
rs28393088	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2840012	0.85[AMR][1000 genomes]
rs28447020	0.84[EUR][1000 genomes]
rs28459407	1.00[AMR][1000 genomes]
rs28473657	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28514442	0.85[AMR][1000 genomes]
rs28522627	0.84[EUR][1000 genomes]
rs28568963	1.00[AMR][1000 genomes]
rs28569075	1.00[AMR][1000 genomes]
rs28569404	0.84[EUR][1000 genomes]
rs28616025	1.00[AMR][1000 genomes]
rs28634932	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28679760	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28706881	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28712432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28882790	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28888757	0.92[AFR][1000 genomes]
rs35917623	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4624185	1.00[AMR][1000 genomes]
rs4788635	0.82[AFR][1000 genomes]
rs55777547	1.00[AMR][1000 genomes]
rs55806458	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57841266	1.00[AMR][1000 genomes]
rs58363387	0.85[AMR][1000 genomes]
rs58819288	1.00[AMR][1000 genomes]
rs59875457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184113	1.00[AMR][1000 genomes]
rs7187532	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7187674	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7188632	0.99[AFR][1000 genomes]
rs7197250	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198345	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7198450	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7200007	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7200263	0.84[EUR][1000 genomes]
rs726887	0.99[AFR][1000 genomes]
rs73582956	0.84[EUR][1000 genomes]
rs73585209	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73587415	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73599411	1.00[AMR][1000 genomes]
rs73601423	1.00[AMR][1000 genomes]
rs74027870	0.84[EUR][1000 genomes]
rs8045319	1.00[AMR][1000 genomes]
rs8046375	1.00[AMR][1000 genomes]
rs8046891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8050489	1.00[AMR][1000 genomes]
rs8051420	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs8051509	0.84[EUR][1000 genomes]
rs8051595	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051982	1.00[AMR][1000 genomes]
rs8052117	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8053288	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057796	1.00[AMR][1000 genomes]
rs8059369	1.00[AMR][1000 genomes]
rs8060309	0.84[EUR][1000 genomes]
rs8063144	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9302636	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9889208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921281	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9921921	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922597	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922853	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9927677	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928119	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9928673	1.00[AMR][1000 genomes]
rs9929864	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9930862	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932125	1.00[AMR][1000 genomes]
rs9933062	1.00[AMR][1000 genomes]
rs9934152	0.85[AMR][1000 genomes]
rs9934365	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9934457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934766	1.00[MEX][hapmap]
rs9936630	0.84[EUR][1000 genomes]
rs9937525	0.85[AMR][1000 genomes]
rs9937973	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9938153	0.90[AFR][1000 genomes]
rs9941341	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv1867	chr16:72352262-72397339	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16970828	TAC1	trans	brain	seeQTL
rs16970828	TMEM155	trans	brain	seeQTL
rs16970828	NELL1	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72345400-72359400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:72347000-72355400	Weak transcription	Gastric	stomach
3	chr16:72352800-72355800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:72353000-72355800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr16:72354200-72358200	Weak transcription	Thymus	Thymus
6	chr16:72354200-72366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:72354200-72366800	Weak transcription	Pancreas	Pancrea
8	chr16:72354200-72368400	Weak transcription	HepG2	liver
9	chr16:72354200-72368600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:72355000-72355600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr16:72355000-72355600	ZNF genes & repeats	Dnd41	blood

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