Variant report

Variant	rs12686312
Chromosome Location	chr9:72944415-72944416
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	chr9:72939453..72941323-chr9:72944240..72946981,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10491653	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1073540	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12683706	0.87[AMR][1000 genomes]
rs12683986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684301	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12684987	0.87[AMR][1000 genomes]
rs12685322	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12685441	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12685491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12685534	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12686573	0.87[AMR][1000 genomes]
rs12686584	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12686850	0.87[AMR][1000 genomes]
rs17051690	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17051696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17052443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17052748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17053503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17088796	0.87[AMR][1000 genomes]
rs17088840	0.87[AMR][1000 genomes]
rs17088889	0.87[AMR][1000 genomes]
rs17088905	0.87[AMR][1000 genomes]
rs1927116	0.87[AMR][1000 genomes]
rs1927117	0.87[AMR][1000 genomes]
rs1927119	0.87[AMR][1000 genomes]
rs1927142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1927148	0.82[ASN][1000 genomes]
rs1927150	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2026138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2148853	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148865	0.87[AMR][1000 genomes]
rs2182732	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296772	0.87[AMR][1000 genomes]
rs2296773	0.87[AMR][1000 genomes]
rs2871295	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34061327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35188046	0.87[AMR][1000 genomes]
rs35508139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3739773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4069793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4287005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4410968	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4439194	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4495496	0.87[AMR][1000 genomes]
rs4596711	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4602958	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4606121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4610818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4621877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56735283	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56860643	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57048128	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57398306	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57477024	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58219953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58662316	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58948879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58969772	0.81[AMR][1000 genomes]
rs58976318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59010963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59444215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59546243	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59589460	0.87[AMR][1000 genomes]
rs59619263	0.87[AMR][1000 genomes]
rs59960592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59976188	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60049462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60391643	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60458589	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61092050	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61265226	0.87[AMR][1000 genomes]
rs61266539	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7046167	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs716535	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs753022	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs753023	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs943540	0.81[ASN][1000 genomes]
rs954808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv1049132	chr9:72895382-73005897	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:72876400-72955200	Weak transcription	Stomach Mucosa	stomach
3	chr9:72891400-72948200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:72912600-72947800	Strong transcription	Placenta	Placenta
5	chr9:72913800-72957800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:72926200-72945000	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:72926400-72965000	Weak transcription	Fetal Brain Male	brain
8	chr9:72926400-72967000	Weak transcription	Fetal Heart	heart
9	chr9:72928200-72948000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:72936000-72970800	Weak transcription	Psoas Muscle	Psoas
11	chr9:72939600-72951200	Weak transcription	K562	blood
12	chr9:72939600-72974000	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:72940000-72948200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:72940200-72944800	Weak transcription	NHEK	skin
15	chr9:72940400-72954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:72940600-72945400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:72941200-72946000	Weak transcription	HMEC	breast
18	chr9:72941200-72965000	Weak transcription	Hela-S3	cervix
19	chr9:72941400-72965200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:72942200-72945000	Strong transcription	Primary T cells from cord blood	blood
21	chr9:72942200-72945000	Strong transcription	Adipose Nuclei	Adipose
22	chr9:72942200-72953800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:72942400-72944800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:72942400-72945000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:72942400-72945000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr9:72942400-72945000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:72942400-72945200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:72942400-72948400	Strong transcription	Fetal Intestine Large	intestine
29	chr9:72942600-72945000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr9:72942600-72945000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:72942600-72945000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:72942600-72948000	Strong transcription	Fetal Kidney	kidney
33	chr9:72942800-72944600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:72942800-72945200	Strong transcription	HSMMtube	muscle
35	chr9:72942800-72945400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:72942800-72961400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:72943000-72944800	Weak transcription	NH-A	brain
38	chr9:72943000-72946200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:72943000-72946400	Weak transcription	HSMM	muscle
40	chr9:72943000-72966400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:72943000-72966600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr9:72943200-72946400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:72943200-72946400	Weak transcription	HUVEC	blood vessel
44	chr9:72943200-72946400	Weak transcription	NHDF-Ad	bronchial
45	chr9:72943200-72968600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:72943400-72945000	Strong transcription	Fetal Lung	lung
47	chr9:72943400-72963400	Weak transcription	HepG2	liver
48	chr9:72943400-72967200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:72943600-72945000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr9:72943600-72945200	Strong transcription	Duodenum Mucosa	Duodenum

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