Variant report

Variant	rs59683461
Chromosome Location	chr12:50927522-50927523
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50926684..50928595-chr12:50975445..50977856,2	MCF-7	breast:
2	chr12:50924997..50928021-chr12:51009408..51011641,3	MCF-7	breast:
3	chr12:50919290..50923217-chr12:50923759..50928110,5	MCF-7	breast:
4	chr12:50926579..50928860-chr12:50929720..50933357,5	MCF-7	breast:
5	chr12:50924992..50927845-chr12:50972241..50975233,2	MCF-7	breast:
6	chr12:50925165..50930036-chr12:51011670..51016786,5	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10506293	0.90[EUR][1000 genomes]
rs10506296	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10735826	0.94[ASN][1000 genomes]
rs10783367	0.91[ASN][1000 genomes]
rs10783368	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876041	0.93[ASN][1000 genomes]
rs10876044	0.92[ASN][1000 genomes]
rs10876048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876054	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876082	0.86[EUR][1000 genomes]
rs10876083	0.86[EUR][1000 genomes]
rs10876088	0.86[EUR][1000 genomes]
rs11169422	0.90[EUR][1000 genomes]
rs11169553	0.86[EUR][1000 genomes]
rs11614911	0.93[ASN][1000 genomes]
rs12099511	0.90[EUR][1000 genomes]
rs12099615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12296379	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307602	0.90[EUR][1000 genomes]
rs12320201	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817256	0.88[ASN][1000 genomes]
rs13328926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1402693	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1521515	0.86[EUR][1000 genomes]
rs1521517	0.95[EUR][1000 genomes]
rs17119774	0.90[EUR][1000 genomes]
rs17124672	0.90[EUR][1000 genomes]
rs17124888	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17124907	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1815010	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1996750	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246840	0.86[EUR][1000 genomes]
rs2252595	0.91[EUR][1000 genomes]
rs2684886	0.86[EUR][1000 genomes]
rs2684890	0.86[EUR][1000 genomes]
rs2684891	0.86[EUR][1000 genomes]
rs2684902	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2684906	0.95[EUR][1000 genomes]
rs2700486	0.86[EUR][1000 genomes]
rs28414775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28479152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2947617	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3803181	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825401	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4129355	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132432	0.82[AMR][1000 genomes]
rs4143663	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4257057	0.90[EUR][1000 genomes]
rs4306347	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4450234	0.90[EUR][1000 genomes]
rs4517607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4562889	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768848	0.85[ASN][1000 genomes]
rs4768885	0.93[ASN][1000 genomes]
rs4768886	0.93[ASN][1000 genomes]
rs4768887	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768894	0.94[ASN][1000 genomes]
rs4768915	0.86[EUR][1000 genomes]
rs4768920	0.86[EUR][1000 genomes]
rs56671180	0.90[EUR][1000 genomes]
rs56753963	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56818625	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57283487	0.90[EUR][1000 genomes]
rs57293958	0.90[EUR][1000 genomes]
rs57328764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57512759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57578212	0.90[EUR][1000 genomes]
rs57811009	0.90[EUR][1000 genomes]
rs57828015	0.90[EUR][1000 genomes]
rs58301497	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58500867	0.90[EUR][1000 genomes]
rs58869591	0.85[EUR][1000 genomes]
rs58888905	0.90[EUR][1000 genomes]
rs58915267	0.85[EUR][1000 genomes]
rs58916974	0.90[EUR][1000 genomes]
rs58943330	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59194948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59284993	0.90[EUR][1000 genomes]
rs59696942	0.90[EUR][1000 genomes]
rs59968707	0.90[EUR][1000 genomes]
rs60010359	0.90[EUR][1000 genomes]
rs60198651	0.90[EUR][1000 genomes]
rs60201334	0.90[EUR][1000 genomes]
rs60239257	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60242613	0.90[EUR][1000 genomes]
rs60396677	0.90[EUR][1000 genomes]
rs60420087	0.90[EUR][1000 genomes]
rs60494920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60743903	0.90[EUR][1000 genomes]
rs60908906	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61578731	0.90[EUR][1000 genomes]
rs6580766	0.86[EUR][1000 genomes]
rs6580767	0.86[EUR][1000 genomes]
rs6580768	0.86[EUR][1000 genomes]
rs7131993	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7132443	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7135222	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301125	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302749	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303202	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7304262	0.90[EUR][1000 genomes]
rs7306387	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310507	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7487645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7955176	0.90[EUR][1000 genomes]
rs7955310	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957060	0.88[ASN][1000 genomes]
rs7969251	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974480	0.90[EUR][1000 genomes]
rs7978443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979184	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979474	0.86[EUR][1000 genomes]
rs939631	0.86[EUR][1000 genomes]
rs951591	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9634264	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9738596	0.96[ASN][1000 genomes]
rs9804759	0.87[EUR][1000 genomes];0.87[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	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50900600-50932000	Weak transcription	Fetal Kidney	kidney
2	chr12:50911600-50939800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:50916400-50931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50918800-50938400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:50920200-50939600	Weak transcription	Fetal Heart	heart
6	chr12:50920400-50931400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:50920800-50929200	Weak transcription	Fetal Stomach	stomach
8	chr12:50920800-50939400	Weak transcription	Fetal Brain Female	brain
9	chr12:50920800-50939800	Weak transcription	Fetal Brain Male	brain
10	chr12:50920800-50962400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:50921000-50929200	Enhancers	Liver	Liver
12	chr12:50921000-50939400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:50921000-50940200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:50921200-50939800	Weak transcription	Brain Germinal Matrix	brain
15	chr12:50922800-50927600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:50923400-50939800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:50923600-50928600	Weak transcription	Ovary	ovary
18	chr12:50923600-50939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:50924000-50927800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:50924000-50929000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr12:50924200-50929200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:50924400-50931400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:50924600-50928800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:50924600-50929200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:50925000-50928600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:50925000-50929000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:50925200-50927600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:50925200-50927600	Enhancers	Pancreas	Pancrea
29	chr12:50925200-50927600	Enhancers	Right Atrium	heart
30	chr12:50925200-50927600	Enhancers	Spleen	Spleen
31	chr12:50925200-50927800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr12:50925200-50928000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:50925200-50928600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:50925200-50928600	Flanking Active TSS	GM12878-XiMat	blood
35	chr12:50925200-50928800	Enhancers	Primary T cells from cord blood	blood
36	chr12:50925200-50928800	Enhancers	Stomach Mucosa	stomach
37	chr12:50925200-50929000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:50925200-50929000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:50925200-50929200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr12:50925200-50929200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:50925200-50929200	Enhancers	Small Intestine	intestine
42	chr12:50925400-50927600	Enhancers	Left Ventricle	heart
43	chr12:50925400-50927800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:50925400-50928200	Enhancers	Primary B cells from cord blood	blood
45	chr12:50925400-50929000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:50925400-50931000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:50925600-50928000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:50925600-50929000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:50925800-50927600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:50925800-50927600	Flanking Active TSS	Hela-S3	cervix

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