Variant report

Variant	rs12946566
Chromosome Location	chr17:67288145-67288146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67286096..67288972-chr17:67296420..67299153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154265	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1011549	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10445224	0.92[ASN][1000 genomes]
rs10491177	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10512526	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11077445	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11649744	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11650658	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11650955	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11651815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651872	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11652207	0.89[ASN][1000 genomes]
rs11654323	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11656389	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11656456	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11869324	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871771	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12449649	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12450167	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12450402	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12450522	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12450743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12452340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12937191	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12937947	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12938039	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12938064	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12938097	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12940364	0.83[ASN][1000 genomes]
rs12941297	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12942763	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12942867	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12943504	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12944980	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12945481	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12945908	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12946776	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12952942	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1550828	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1558168	0.92[ASN][1000 genomes]
rs15886	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1990248	0.82[ASN][1000 genomes]
rs2364996	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2441358	0.87[ASN][1000 genomes]
rs34334829	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34609440	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34985085	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4310935	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4310936	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs476677	0.81[ASN][1000 genomes]
rs481876	0.86[ASN][1000 genomes]
rs486840	0.88[ASN][1000 genomes]
rs488714	0.81[ASN][1000 genomes]
rs494946	0.81[ASN][1000 genomes]
rs523505	0.83[ASN][1000 genomes]
rs544940	0.88[ASN][1000 genomes]
rs557491	0.95[ASN][1000 genomes]
rs55773491	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs568536	0.88[ASN][1000 genomes]
rs57949169	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58634970	0.83[EUR][1000 genomes]
rs7223895	0.84[ASN][1000 genomes]
rs7225762	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs817126	0.84[ASN][1000 genomes]
rs817127	0.86[ASN][1000 genomes]
rs9646388	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv1063768	chr17:67268342-67311136	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
9	esv1799828	chr17:67280310-67309039	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
3	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
4	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
8	chr17:67250000-67289200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:67251600-67289200	Weak transcription	Brain Anterior Caudate	brain
10	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:67265000-67289200	Weak transcription	Lung	lung
12	chr17:67265000-67289800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:67266200-67290000	Weak transcription	Fetal Heart	heart
14	chr17:67266200-67310400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:67268600-67295400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:67270200-67307400	Weak transcription	Colonic Mucosa	Colon
17	chr17:67270600-67289600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr17:67271000-67289200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:67271000-67298600	Weak transcription	Fetal Lung	lung
20	chr17:67271400-67296000	Weak transcription	Fetal Kidney	kidney
21	chr17:67272400-67306400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr17:67272800-67289200	Weak transcription	Pancreas	Pancrea
23	chr17:67274600-67288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr17:67275800-67289200	Weak transcription	Fetal Muscle Leg	muscle
25	chr17:67276200-67289200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:67276400-67310600	Weak transcription	Brain Substantia Nigra	brain
27	chr17:67276600-67308800	Weak transcription	Aorta	Aorta
28	chr17:67277200-67289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:67277600-67288600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:67277600-67289000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr17:67277600-67289200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:67277600-67289200	Strong transcription	Liver	Liver
33	chr17:67277600-67293600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:67277800-67297000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:67278000-67292000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:67278200-67297600	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:67278400-67291000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr17:67278600-67289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:67279400-67308000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr17:67279600-67306400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:67279800-67289200	Weak transcription	Colon Smooth Muscle	Colon
42	chr17:67279800-67293600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:67280000-67307200	Weak transcription	Fetal Thymus	thymus
44	chr17:67281200-67288800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr17:67281600-67289200	Weak transcription	GM12878-XiMat	blood
46	chr17:67281600-67289400	Weak transcription	Brain Angular Gyrus	brain
47	chr17:67281800-67289200	Weak transcription	Spleen	Spleen
48	chr17:67283600-67297800	Weak transcription	Stomach Mucosa	stomach
49	chr17:67283600-67304800	Weak transcription	NHDF-Ad	bronchial
50	chr17:67283800-67288600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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