Variant report

Variant	rs4788664
Chromosome Location	chr16:72880564-72880565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72878570..72880938-chr16:73094933..73097735,2	MCF-7	breast:
2	chr16:72877476..72879794-chr16:72879861..72883211,4	MCF-7	breast:
3	chr16:72878526..72882353-chr16:72945931..72948591,3	MCF-7	breast:
4	chr16:72879898..72883074-chr16:73230145..73232683,3	MCF-7	breast:
5	chr16:72866473..72867074-chr16:72880127..72880808,2	MCF-7	breast:
6	chr16:72875132..72886767-chr16:73085117..73094489,23	MCF-7	breast:
7	chr16:72874196..72876790-chr16:72878784..72881907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272250	Chromatin interaction
ENSG00000271009	Chromatin interaction
ENSG00000140836	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1035983	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1035984	0.86[AMR][1000 genomes]
rs10400973	1.00[AFR][1000 genomes]
rs10492826	0.86[AMR][1000 genomes]
rs11075940	1.00[AFR][1000 genomes]
rs11640709	0.81[JPT][hapmap]
rs12051226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12103361	0.90[MEX][hapmap];0.88[AMR][1000 genomes]
rs12595874	1.00[MEX][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs12596196	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12597202	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12597703	1.00[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12598003	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12598048	0.88[AMR][1000 genomes]
rs12598858	0.88[AMR][1000 genomes]
rs12599442	1.00[ASW][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs12599589	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12600293	0.96[AMR][1000 genomes]
rs12708932	1.00[AFR][1000 genomes]
rs12921040	1.00[AFR][1000 genomes]
rs13332877	0.90[AMR][1000 genomes]
rs13333025	0.93[AMR][1000 genomes]
rs1366846	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1366847	1.00[AFR][1000 genomes]
rs1429434	1.00[AFR][1000 genomes]
rs1544964	1.00[AFR][1000 genomes]
rs16971279	0.88[AMR][1000 genomes]
rs16971281	0.88[AMR][1000 genomes]
rs16971287	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16971288	0.88[AMR][1000 genomes]
rs16971290	0.88[AMR][1000 genomes]
rs16971292	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16971306	1.00[ASW][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs16971312	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16971314	0.93[AMR][1000 genomes]
rs16971315	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16971318	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs16971321	1.00[ASW][hapmap];0.96[AMR][1000 genomes]
rs16971324	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971325	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1859593	0.81[AMR][1000 genomes]
rs1990096	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2040939	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2040940	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2043022	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2115625	1.00[AFR][1000 genomes]
rs2229286	1.00[ASW][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs2229290	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2266932	1.00[ASW][hapmap];0.95[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2266934	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2266935	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2266936	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2266938	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2266939	0.95[AMR][1000 genomes]
rs2266941	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2266942	0.95[AMR][1000 genomes]
rs2266944	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2358805	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2358811	0.88[AMR][1000 genomes]
rs2358812	0.88[AMR][1000 genomes]
rs292913	0.83[AMR][1000 genomes]
rs292914	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs292915	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs292916	0.81[AMR][1000 genomes]
rs292917	0.84[AMR][1000 genomes]
rs292918	0.83[AMR][1000 genomes]
rs292919	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs292920	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs292921	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs292922	0.84[AMR][1000 genomes]
rs292923	0.84[AMR][1000 genomes]
rs292924	0.84[AMR][1000 genomes]
rs292925	0.84[AMR][1000 genomes]
rs292926	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs292927	0.84[AMR][1000 genomes]
rs292928	0.84[AMR][1000 genomes]
rs292929	0.84[AMR][1000 genomes]
rs292930	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292931	0.88[AMR][1000 genomes]
rs292932	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292933	0.88[AMR][1000 genomes]
rs292934	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292935	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292937	0.88[AMR][1000 genomes]
rs292938	0.88[AMR][1000 genomes]
rs292939	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292940	0.88[AMR][1000 genomes]
rs292941	0.88[AMR][1000 genomes]
rs292942	0.88[AMR][1000 genomes]
rs292943	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292945	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292946	0.88[AMR][1000 genomes]
rs292947	0.88[AMR][1000 genomes]
rs3812983	1.00[ASW][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs4238966	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4278755	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4788479	0.95[AMR][1000 genomes]
rs4788655	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4788657	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4788663	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4788665	0.86[JPT][hapmap]
rs4788666	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4788667	1.00[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788669	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59254438	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs60974482	0.88[AMR][1000 genomes]
rs6416744	1.00[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499578	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6499579	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6499581	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs6499591	1.00[ASW][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499592	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6499593	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs714101	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs714102	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7187123	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7194567	1.00[AFR][1000 genomes]
rs7198782	0.85[AMR][1000 genomes]
rs7206490	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740177	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs8044614	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8059268	1.00[AFR][1000 genomes]
rs9302640	1.00[AFR][1000 genomes]
rs982799	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9921081	0.93[AMR][1000 genomes]
rs9923006	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9927280	1.00[AFR][1000 genomes]
rs9933433	0.87[AMR][1000 genomes]
rs9934215	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9935202	1.00[AFR][1000 genomes]
rs9935250	1.00[AFR][1000 genomes]
rs9936708	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72862600-72882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:72867600-72892400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:72868600-72881400	Weak transcription	Hela-S3	cervix
4	chr16:72871000-72881800	Weak transcription	Liver	Liver
5	chr16:72872200-72883600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:72872400-72881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:72872600-72881400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr16:72872800-72880800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:72872800-72881400	Weak transcription	NH-A	brain
10	chr16:72873200-72891800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:72873400-72881800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr16:72873600-72881400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr16:72875000-72882200	Weak transcription	Stomach Mucosa	stomach
14	chr16:72875000-72882400	Weak transcription	Gastric	stomach
15	chr16:72875200-72881800	Weak transcription	Ovary	ovary
16	chr16:72875400-72880800	Weak transcription	Brain Substantia Nigra	brain
17	chr16:72875400-72882600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr16:72875600-72883000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:72875800-72880800	Weak transcription	Brain Angular Gyrus	brain
20	chr16:72875800-72880800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:72875800-72881000	Weak transcription	Fetal Brain Male	brain
22	chr16:72875800-72881200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr16:72875800-72881200	Weak transcription	Adipose Nuclei	Adipose
24	chr16:72875800-72881800	Weak transcription	Fetal Kidney	kidney
25	chr16:72876000-72881000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:72876000-72881200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr16:72876000-72881200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr16:72876400-72881200	Weak transcription	Osteobl	bone
29	chr16:72876800-72882400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:72877400-72883600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:72877600-72881000	Strong transcription	HepG2	liver
32	chr16:72877600-72881600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:72877800-72880800	Enhancers	Primary hematopoietic stem cells	blood
34	chr16:72877800-72882600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr16:72877800-72885400	Enhancers	Fetal Muscle Leg	muscle
36	chr16:72878000-72882000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr16:72878000-72883000	Enhancers	Fetal Heart	heart
38	chr16:72878000-72885800	Enhancers	Fetal Muscle Trunk	muscle
39	chr16:72878200-72880600	Enhancers	Primary B cells from peripheral blood	blood
40	chr16:72878200-72882400	Enhancers	Left Ventricle	heart
41	chr16:72878200-72882400	Enhancers	Right Ventricle	heart
42	chr16:72878400-72881200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr16:72878400-72881200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr16:72878400-72881800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr16:72878600-72881000	Strong transcription	Fetal Intestine Small	intestine
46	chr16:72878600-72881600	Weak transcription	Fetal Lung	lung
47	chr16:72878800-72883400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr16:72879000-72880600	Enhancers	Psoas Muscle	Psoas
49	chr16:72879000-72880800	Weak transcription	Brain Anterior Caudate	brain
50	chr16:72879000-72881600	Weak transcription	Brain Germinal Matrix	brain

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