Variant report

Variant	rs12599589
Chromosome Location	chr16:72886049-72886050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72874571..72877470-chr16:72881574..72886703,5	MCF-7	breast:
2	chr16:72884109..72886413-chr16:72900288..72901895,2	MCF-7	breast:
3	chr16:72883594..72886259-chr16:72953708..72956575,2	MCF-7	breast:
4	chr16:72885635..72887745-chr20:10163080..10164929,2	MCF-7	breast:
5	chr16:72875132..72886767-chr16:73085117..73094489,23	MCF-7	breast:

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

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1035983	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1035984	0.89[AMR][1000 genomes]
rs10400973	1.00[AFR][1000 genomes]
rs10492826	0.89[AMR][1000 genomes]
rs11075940	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11640709	0.83[JPT][hapmap]
rs12051226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12103361	0.91[AMR][1000 genomes]
rs12595874	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs12596196	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12597202	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12597703	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12598003	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12598048	0.91[AMR][1000 genomes]
rs12598858	0.91[AMR][1000 genomes]
rs12599442	0.96[AMR][1000 genomes]
rs12600293	0.96[AMR][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];0.89[AMR][1000 genomes]
rs1429431	0.80[AMR][1000 genomes]
rs1429432	0.80[AMR][1000 genomes]
rs1429434	1.00[AFR][1000 genomes]
rs1544964	1.00[AFR][1000 genomes]
rs16971279	0.91[AMR][1000 genomes]
rs16971281	0.91[AMR][1000 genomes]
rs16971287	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16971288	0.91[AMR][1000 genomes]
rs16971290	0.91[AMR][1000 genomes]
rs16971292	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16971306	0.96[AMR][1000 genomes]
rs16971312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs16971314	0.96[AMR][1000 genomes]
rs16971315	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs16971318	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs16971321	0.96[AMR][1000 genomes]
rs16971324	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971325	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1859593	0.85[AMR][1000 genomes]
rs1990096	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2040939	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2040940	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2043022	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2115625	1.00[AFR][1000 genomes]
rs2229286	0.95[AMR][1000 genomes]
rs2229290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2266932	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	0.98[AMR][1000 genomes]
rs2266941	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2266942	0.98[AMR][1000 genomes]
rs2266944	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2358805	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2358811	0.91[AMR][1000 genomes]
rs2358812	0.91[AMR][1000 genomes]
rs292913	0.86[AMR][1000 genomes]
rs292914	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292915	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292916	0.84[AMR][1000 genomes]
rs292917	0.88[AMR][1000 genomes]
rs292918	0.86[AMR][1000 genomes]
rs292919	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs292920	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292921	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292922	0.88[AMR][1000 genomes]
rs292923	0.88[AMR][1000 genomes]
rs292924	0.88[AMR][1000 genomes]
rs292925	0.88[AMR][1000 genomes]
rs292926	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs292927	0.88[AMR][1000 genomes]
rs292928	0.88[AMR][1000 genomes]
rs292929	0.88[AMR][1000 genomes]
rs292930	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292931	0.91[AMR][1000 genomes]
rs292932	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292933	0.91[AMR][1000 genomes]
rs292934	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292935	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292937	0.91[AMR][1000 genomes]
rs292938	0.91[AMR][1000 genomes]
rs292939	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292940	0.91[AMR][1000 genomes]
rs292941	0.91[AMR][1000 genomes]
rs292942	0.91[AMR][1000 genomes]
rs292943	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292945	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs292946	0.91[AMR][1000 genomes]
rs292947	0.91[AMR][1000 genomes]
rs3812983	0.89[AMR][1000 genomes]
rs4238966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4278755	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4788479	0.98[AMR][1000 genomes]
rs4788655	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4788657	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4788663	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs4788664	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]
rs4788665	0.86[JPT][hapmap]
rs4788666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4788667	0.93[CHB][hapmap];1.00[JPT][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];0.91[AMR][1000 genomes]
rs60974482	0.91[AMR][1000 genomes]
rs6416744	0.93[CHB][hapmap];1.00[JPT][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];0.86[AMR][1000 genomes]
rs6499579	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6499581	1.00[AFR][1000 genomes]
rs6499591	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499592	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6499593	0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs714101	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs714102	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7187123	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7194567	1.00[AFR][1000 genomes]
rs7198782	0.85[AMR][1000 genomes]
rs7203232	0.80[AMR][1000 genomes]
rs7206490	0.85[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	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs740177	0.81[JPT][hapmap]
rs8044614	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8059268	1.00[AFR][1000 genomes]
rs9302640	1.00[AFR][1000 genomes]
rs982799	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9921081	0.93[AMR][1000 genomes]
rs9923006	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9927280	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9933433	0.87[AMR][1000 genomes]
rs9934215	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9936708	1.00[AFR][1000 genomes];0.81[AMR][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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72867600-72892400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:72873200-72891800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:72882400-72886800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:72882400-72887400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr16:72882400-72887600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:72882400-72891800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:72883200-72887600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:72883200-72899200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:72883200-72909200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr16:72883400-72886600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr16:72883400-72887200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr16:72883400-72887800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr16:72883400-72888000	Weak transcription	Spleen	Spleen
14	chr16:72883400-72891800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr16:72883400-72892200	Weak transcription	Brain Angular Gyrus	brain
16	chr16:72883400-72898400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:72883400-72898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr16:72883400-72908400	Weak transcription	Fetal Intestine Large	intestine
19	chr16:72883400-72918800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:72883600-72887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:72883600-72887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:72883600-72887400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:72883600-72887400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:72883600-72887600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:72883600-72887600	Weak transcription	Brain Germinal Matrix	brain
26	chr16:72883600-72887800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr16:72883600-72887800	Weak transcription	Brain Anterior Caudate	brain
28	chr16:72883600-72890800	Weak transcription	Brain Substantia Nigra	brain
29	chr16:72883600-72891000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:72883600-72892200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:72883600-72892400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr16:72883600-72893200	Weak transcription	Fetal Intestine Small	intestine
33	chr16:72883600-72912200	Weak transcription	Ovary	ovary
34	chr16:72883800-72908800	Weak transcription	Hela-S3	cervix
35	chr16:72884200-72886800	Weak transcription	HepG2	liver
36	chr16:72884200-72891400	Weak transcription	Pancreas	Pancrea
37	chr16:72884200-72892000	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:72884200-72899200	Weak transcription	Liver	Liver
39	chr16:72884200-72902200	Weak transcription	Right Ventricle	heart
40	chr16:72884200-72911600	Weak transcription	Gastric	stomach
41	chr16:72884400-72887600	Weak transcription	Aorta	Aorta
42	chr16:72884400-72892800	Weak transcription	Fetal Heart	heart
43	chr16:72884600-72887400	Weak transcription	Fetal Kidney	kidney
44	chr16:72885000-72886200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr16:72885000-72887800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr16:72885200-72886800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:72885200-72887800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr16:72885200-72888000	Weak transcription	Brain Hippocampus Middle	brain
49	chr16:72885200-72891400	Weak transcription	Right Atrium	heart
50	chr16:72885200-72892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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