Variant report

Variant	rs7299002
Chromosome Location	chr12:50095459-50095460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50094765..50096315-chr12:50134096..50136902,2	K562	blood:
2	chr12:50094601..50096725-chr12:50097954..50101430,3	MCF-7	breast:
3	chr12:50035243..50038149-chr12:50095334..50097229,2	MCF-7	breast:
4	chr12:50080608..50083488-chr12:50095334..50097821,2	MCF-7	breast:
5	chr12:50093739..50096760-chr12:50100388..50102925,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1049986	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875968	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11169069	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169073	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169076	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169081	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169082	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169092	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169097	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169101	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169104	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169106	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169109	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169111	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169112	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169113	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169118	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169125	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169127	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169133	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169140	0.85[AMR][1000 genomes]
rs11615488	0.92[ASN][1000 genomes]
rs11833411	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11834380	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12296586	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299505	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12299513	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12301824	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12303310	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304796	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12305460	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12308256	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12309940	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310510	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311839	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12314795	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314878	0.83[ASN][1000 genomes]
rs12315224	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315791	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316284	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12317646	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317778	0.80[EUR][1000 genomes]
rs12320556	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12321169	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12321819	0.83[ASN][1000 genomes]
rs13066	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13906	0.83[ASN][1000 genomes]
rs1470906	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574326	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123808	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2005195	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241418	0.83[ASN][1000 genomes]
rs2278068	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278069	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278070	0.80[ASN][1000 genomes]
rs2303305	0.80[ASN][1000 genomes]
rs2336058	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878532	0.81[AMR][1000 genomes]
rs3815832	0.83[ASN][1000 genomes]
rs3887728	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4045193	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4133070	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584654	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs52824916	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55853522	0.83[ASN][1000 genomes]
rs57191490	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57342147	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57463238	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57916875	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58278271	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58446833	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59233136	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59849800	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59940006	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60121503	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60402517	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61616163	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61620972	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61710637	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580719	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131915	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136052	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137976	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296281	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7301209	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7306877	0.83[ASN][1000 genomes]
rs7309607	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7312658	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7313738	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305008	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305012	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305085	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73305098	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73306808	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309030	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74089182	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7688	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952734	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953911	0.83[ASN][1000 genomes]
rs7954994	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955586	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7956089	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956181	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962645	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962863	0.89[ASN][1000 genomes]
rs7963954	0.89[ASN][1000 genomes]
rs7965658	0.81[ASN][1000 genomes]
rs7967624	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970241	0.83[ASN][1000 genomes]
rs7973389	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975599	0.83[ASN][1000 genomes]
rs7977389	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979262	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980979	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876889	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs897056	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9804749	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804971	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:50091200-50096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:50093000-50096400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:50093200-50095600	Weak transcription	Stomach Mucosa	stomach
5	chr12:50093200-50095800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50093200-50096400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:50093200-50096400	Weak transcription	Brain Angular Gyrus	brain
8	chr12:50093200-50096400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:50093200-50096600	Weak transcription	Ovary	ovary
10	chr12:50093200-50096800	Weak transcription	Small Intestine	intestine
11	chr12:50093200-50097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:50093200-50098200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:50093200-50098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:50093200-50098800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:50093200-50099200	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:50093200-50099600	Weak transcription	Fetal Heart	heart
17	chr12:50093200-50100200	Weak transcription	Esophagus	oesophagus
18	chr12:50093400-50095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:50093400-50095600	Weak transcription	Placenta	Placenta
20	chr12:50093400-50095800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:50093400-50095800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:50093400-50095800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:50093400-50095800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:50093400-50095800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:50093400-50095800	Weak transcription	Fetal Lung	lung
26	chr12:50093400-50095800	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:50093400-50095800	Weak transcription	Fetal Thymus	thymus
28	chr12:50093400-50095800	Weak transcription	Left Ventricle	heart
29	chr12:50093400-50095800	Weak transcription	Spleen	Spleen
30	chr12:50093400-50096200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:50093400-50096400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:50093400-50096400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:50093400-50096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:50093400-50096400	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:50093400-50096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:50093400-50096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:50093400-50096400	Weak transcription	NHDF-Ad	bronchial
38	chr12:50093400-50096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:50093400-50096600	Weak transcription	Psoas Muscle	Psoas
40	chr12:50093400-50096600	Weak transcription	Right Atrium	heart
41	chr12:50093400-50096600	Weak transcription	Thymus	Thymus
42	chr12:50093400-50096800	Weak transcription	HMEC	breast
43	chr12:50093400-50097000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:50093400-50097000	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:50093400-50097000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:50093400-50097000	Weak transcription	K562	blood
47	chr12:50093400-50097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:50093400-50097200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:50093400-50097400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:50093400-50098600	Weak transcription	Right Ventricle	heart

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