Variant report

Variant	rs59599274
Chromosome Location	chr3:51381391-51381392
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51376546..51378472-chr3:51379958..51381603,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs17051747	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55640023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55699461	1.00[EUR][1000 genomes]
rs55708856	1.00[EUR][1000 genomes]
rs56037427	1.00[EUR][1000 genomes]
rs56254449	1.00[EUR][1000 genomes]
rs56361536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56870664	1.00[EUR][1000 genomes]
rs56940802	1.00[EUR][1000 genomes]
rs57569631	0.93[AFR][1000 genomes]
rs57742040	1.00[EUR][1000 genomes]
rs58236908	1.00[EUR][1000 genomes]
rs58548979	1.00[EUR][1000 genomes]
rs59019902	1.00[EUR][1000 genomes]
rs59557845	1.00[EUR][1000 genomes]
rs59652730	1.00[EUR][1000 genomes]
rs59794491	1.00[EUR][1000 genomes]
rs60166061	1.00[EUR][1000 genomes]
rs60862896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60973580	1.00[EUR][1000 genomes]
rs61337570	1.00[EUR][1000 genomes]
rs61526358	1.00[EUR][1000 genomes]
rs61570923	1.00[EUR][1000 genomes]
rs6781959	1.00[EUR][1000 genomes]
rs6799213	1.00[EUR][1000 genomes]
rs6804101	1.00[EUR][1000 genomes]
rs73833980	1.00[EUR][1000 genomes]
rs73833981	1.00[EUR][1000 genomes]
rs73833982	1.00[EUR][1000 genomes]
rs73833985	1.00[EUR][1000 genomes]
rs73833986	1.00[EUR][1000 genomes]
rs73833987	1.00[EUR][1000 genomes]
rs73833989	1.00[EUR][1000 genomes]
rs73833990	1.00[EUR][1000 genomes]
rs73833991	1.00[EUR][1000 genomes]
rs73833992	1.00[EUR][1000 genomes]
rs73833993	1.00[EUR][1000 genomes]
rs73833996	1.00[EUR][1000 genomes]
rs73834257	1.00[EUR][1000 genomes]
rs73837406	1.00[EUR][1000 genomes]
rs73837420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837421	1.00[EUR][1000 genomes]
rs73837422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837423	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837425	1.00[EUR][1000 genomes]
rs73837428	1.00[EUR][1000 genomes]
rs73837431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73837434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7635095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9990213	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
2	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:51378200-51383000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:51378400-51382600	Weak transcription	Spleen	Spleen
7	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:51378600-51383000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:51378800-51381400	Weak transcription	Esophagus	oesophagus
11	chr3:51378800-51381600	Weak transcription	Gastric	stomach
12	chr3:51378800-51381600	Weak transcription	Stomach Mucosa	stomach
13	chr3:51378800-51382000	Enhancers	Hela-S3	cervix
14	chr3:51378800-51383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:51378800-51387400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:51378800-51388000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
18	chr3:51379000-51381400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:51379000-51381400	Weak transcription	NHEK	skin
20	chr3:51379000-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:51379000-51386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
25	chr3:51379200-51381400	Weak transcription	HMEC	breast
26	chr3:51379200-51381600	Weak transcription	NH-A	brain
27	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:51379400-51381400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:51379400-51381400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:51379400-51381400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:51379400-51382200	Weak transcription	Placenta	Placenta
34	chr3:51379400-51383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:51379600-51381400	Weak transcription	Osteobl	bone
37	chr3:51379800-51381800	Strong transcription	Fetal Brain Female	brain
38	chr3:51379800-51382200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
41	chr3:51380200-51383000	Enhancers	A549	lung
42	chr3:51380600-51382400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:51380800-51381400	Strong transcription	Brain Anterior Caudate	brain
44	chr3:51380800-51383000	Strong transcription	Brain Hippocampus Middle	brain
45	chr3:51381000-51381800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:51381000-51383000	Enhancers	NHLF	lung
47	chr3:51381200-51381400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:51381200-51382000	Enhancers	HSMMtube	muscle
49	chr3:51381200-51382600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:51381200-51382600	Enhancers	HSMM	muscle

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