Variant report

Variant	rs2040940
Chromosome Location	chr16:72807413-72807414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72800047..72802157-chr16:72806657..72808426,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFHX3-1	chr16:72807234-72807445	l_1360_chr16:72783804-72807057_testes

Extended variants
information (count: 165 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1035983	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1035984	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10400973	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10492826	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075938	0.83[AFR][1000 genomes]
rs11075940	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12051226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12051305	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12051376	1.00[AFR][1000 genomes]
rs12051436	1.00[AFR][1000 genomes]
rs12103361	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12445485	1.00[AFR][1000 genomes]
rs12595874	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12596196	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12597202	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12597703	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12598003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12598048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12598858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12599442	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12599589	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12600293	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12708932	1.00[AFR][1000 genomes]
rs12921040	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13332877	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13333025	0.85[AMR][1000 genomes]
rs1366846	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1366847	1.00[AFR][1000 genomes]
rs1429431	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1429432	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1429433	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1429434	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1529527	1.00[AFR][1000 genomes]
rs1544964	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16971281	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16971306	0.94[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16971312	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971314	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971318	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16971321	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16971324	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs16971325	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1859593	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990096	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2040939	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2043022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2115625	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2115626	0.80[ASN][1000 genomes]
rs2163067	1.00[AFR][1000 genomes]
rs2229286	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2229290	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2266932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266934	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266935	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266936	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266938	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266939	0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2266941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2266942	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266944	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358805	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2358811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884552	1.00[AFR][1000 genomes]
rs2914768	1.00[AFR][1000 genomes]
rs2914770	1.00[AFR][1000 genomes]
rs2914772	1.00[AFR][1000 genomes]
rs2914773	1.00[AFR][1000 genomes]
rs2914778	1.00[AFR][1000 genomes]
rs292913	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292914	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292915	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292916	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292917	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292918	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292919	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292920	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292921	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs292922	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292924	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292925	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292926	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292927	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292929	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs292930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs292937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs292938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs292939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs292940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292941	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs292942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs292943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs292945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs292946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs292947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967238	1.00[AFR][1000 genomes]
rs2967239	1.00[AFR][1000 genomes]
rs3812983	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4238966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4278755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4788474	1.00[AFR][1000 genomes]
rs4788479	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4788655	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788657	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4788664	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4788666	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4788667	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4788669	0.88[AMR][1000 genomes]
rs59254438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60974482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6416744	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6499575	1.00[AFR][1000 genomes]
rs6499576	1.00[AFR][1000 genomes]
rs6499578	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6499579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6499581	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6499591	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6499592	0.88[AMR][1000 genomes]
rs6499593	0.89[AMR][1000 genomes]
rs714101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs714102	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7187123	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7192128	1.00[AFR][1000 genomes]
rs7194567	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7198782	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7199644	0.81[ASN][1000 genomes]
rs7199653	0.81[ASN][1000 genomes]
rs7203205	0.82[ASN][1000 genomes]
rs7203232	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7206490	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs740176	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs74028108	1.00[ASN][1000 genomes]
rs8044614	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8053419	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8059268	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9302640	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs982799	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9921081	0.85[AMR][1000 genomes]
rs9923006	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9924937	0.81[ASN][1000 genomes]
rs9927280	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9933433	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9934215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9935202	1.00[AFR][1000 genomes]
rs9935250	1.00[AFR][1000 genomes]
rs9936708	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs999210	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1063049	chr16:72577004-72887111	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv542952	chr16:72577004-72887111	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1868	chr16:72801962-72820054	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72783800-72810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:72794800-72818000	Weak transcription	Aorta	Aorta
3	chr16:72798400-72817800	Weak transcription	HSMM	muscle
4	chr16:72798800-72815600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:72801000-72808000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:72803000-72811200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:72803400-72808800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr16:72803600-72809800	Weak transcription	Primary T cells from cord blood	blood
9	chr16:72806400-72809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:72806400-72820600	Weak transcription	Fetal Intestine Small	intestine

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