Variant report

Variant	rs58023472
Chromosome Location	chr12:49303910-49303911
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49292727..49295462-chr12:49303165..49304896,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1051886	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1054376	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747556	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747557	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747558	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783289	0.95[ASN][1000 genomes]
rs10783290	0.93[ASN][1000 genomes]
rs10783292	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783293	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10783294	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783295	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783297	0.92[ASN][1000 genomes]
rs10875886	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875888	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875892	0.81[ASN][1000 genomes]
rs10875893	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875894	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875895	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875896	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875897	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875898	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875900	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875901	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875902	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1111662	0.92[ASN][1000 genomes]
rs11168779	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168784	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168790	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168792	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168794	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168795	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168797	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168798	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168800	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168801	0.85[ASN][1000 genomes]
rs11168803	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168811	0.80[ASN][1000 genomes]
rs11168812	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608916	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610459	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610497	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614474	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227240	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12228521	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229275	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423542	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579249	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1318692	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690182	0.90[ASN][1000 genomes]
rs1818996	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1830192	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030900	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070940	0.90[ASN][1000 genomes]
rs2073480	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131713	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272311	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272312	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293449	0.97[ASN][1000 genomes]
rs2368701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453063	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2463175	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641450	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2694839	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2694840	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741627	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759146	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782353	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809147	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825182	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825184	0.99[ASN][1000 genomes]
rs4018510	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237854	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4433614	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4526804	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760600	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760647	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760661	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760662	0.84[EUR][1000 genomes]
rs4760663	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760664	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760665	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760666	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760667	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760668	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59087236	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61941142	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61942166	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942167	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61942169	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942207	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942209	0.81[ASN][1000 genomes]
rs6580696	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134686	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297958	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7298330	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304942	1.00[ASN][1000 genomes]
rs7313988	0.90[ASN][1000 genomes]
rs7489036	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963018	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7963160	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7976473	0.86[ASN][1000 genomes]
rs833820	0.90[ASN][1000 genomes]
rs833821	0.90[ASN][1000 genomes]
rs833822	0.90[ASN][1000 genomes]
rs833827	0.90[ASN][1000 genomes]
rs833828	0.88[ASN][1000 genomes]
rs833839	0.84[ASN][1000 genomes]
rs833840	0.84[ASN][1000 genomes]
rs833841	0.83[ASN][1000 genomes]
rs833842	0.83[ASN][1000 genomes]
rs833843	0.80[ASN][1000 genomes]
rs961320	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9645813	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783452	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783477	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788029	0.96[ASN][1000 genomes]
rs9795742	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9796008	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58023472	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49298200-49315800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:49298200-49318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:49298400-49308000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:49298400-49310400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49298400-49310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:49298400-49310400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:49298400-49310600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:49298400-49310600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:49298400-49310800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:49298400-49310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:49298400-49311400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:49298400-49313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:49298400-49314800	Weak transcription	Lung	lung
14	chr12:49298400-49315000	Weak transcription	Osteobl	bone
15	chr12:49298400-49317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:49298400-49318000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:49298400-49318000	Weak transcription	Brain Substantia Nigra	brain
18	chr12:49298400-49318000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:49298400-49318200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:49298400-49318200	Weak transcription	Right Atrium	heart
21	chr12:49298400-49318400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:49298600-49310400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:49298600-49315000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:49298600-49315000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:49298600-49316000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:49298600-49318200	Weak transcription	Brain Anterior Caudate	brain
27	chr12:49298800-49307800	Weak transcription	Fetal Stomach	stomach
28	chr12:49298800-49308400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:49298800-49315400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:49298800-49315800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:49298800-49318000	Weak transcription	Fetal Lung	lung
32	chr12:49298800-49318200	Weak transcription	Fetal Brain Male	brain
33	chr12:49299400-49315000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:49301200-49304800	Enhancers	Fetal Intestine Large	intestine
35	chr12:49301800-49305400	Enhancers	HepG2	liver
36	chr12:49301800-49315600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:49302000-49318200	Weak transcription	Brain Germinal Matrix	brain
38	chr12:49302200-49315400	Weak transcription	Pancreas	Pancrea
39	chr12:49302800-49311400	Weak transcription	HSMMtube	muscle
40	chr12:49302800-49317800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:49303800-49304200	Enhancers	A549	lung
42	chr12:49303800-49304800	Enhancers	Fetal Intestine Small	intestine

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