Variant report

Variant	rs28525383
Chromosome Location	chr3:17678986-17678987
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17677327..17679225-chr3:17680575..17682681,2	K562	blood:
2	chr3:17667671..17669916-chr3:17678475..17680012,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs11914537	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11914797	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11915560	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11916424	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916984	1.00[EUR][1000 genomes]
rs11921699	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11922861	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923635	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11924147	1.00[EUR][1000 genomes]
rs11924560	1.00[EUR][1000 genomes]
rs11925226	1.00[EUR][1000 genomes]
rs11925353	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926087	1.00[EUR][1000 genomes]
rs11926251	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927232	1.00[EUR][1000 genomes]
rs11927283	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929046	1.00[EUR][1000 genomes]
rs11929521	1.00[EUR][1000 genomes]
rs12106899	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12106900	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12107061	1.00[EUR][1000 genomes]
rs12152509	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12185952	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57352109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58152540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58392667	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58777809	1.00[EUR][1000 genomes]
rs58848058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58921548	1.00[EUR][1000 genomes]
rs59582994	0.87[AMR][1000 genomes]
rs59891221	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59960076	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60245392	1.00[EUR][1000 genomes]
rs60459720	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60662240	1.00[EUR][1000 genomes]
rs60803166	1.00[EUR][1000 genomes]
rs60838916	1.00[EUR][1000 genomes]
rs60940413	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61650046	1.00[EUR][1000 genomes]
rs61698855	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577595	1.00[EUR][1000 genomes]
rs6577629	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763348	1.00[EUR][1000 genomes]
rs6789382	1.00[EUR][1000 genomes]
rs6796915	1.00[EUR][1000 genomes]
rs73160940	0.87[AMR][1000 genomes]
rs73160942	0.87[AMR][1000 genomes]
rs73160943	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160950	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160951	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160957	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160964	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160967	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73161427	1.00[EUR][1000 genomes]
rs73161452	1.00[EUR][1000 genomes]
rs73164768	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164796	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165722	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165729	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165734	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165735	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165740	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165764	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165771	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165775	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165777	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165779	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165792	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73166516	1.00[EUR][1000 genomes]
rs73166544	1.00[EUR][1000 genomes]
rs73167503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73167510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167513	1.00[EUR][1000 genomes]
rs73167514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167523	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167527	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73168748	1.00[EUR][1000 genomes]
rs73168752	1.00[EUR][1000 genomes]
rs73170844	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170845	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170855	1.00[EUR][1000 genomes]
rs73170858	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170877	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170878	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73172909	1.00[EUR][1000 genomes]
rs73172914	1.00[EUR][1000 genomes]
rs73172924	1.00[EUR][1000 genomes]
rs7619879	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7620585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621577	1.00[EUR][1000 genomes]
rs7630381	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631803	1.00[EUR][1000 genomes]
rs7648122	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9680896	1.00[EUR][1000 genomes]
rs9754654	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9754657	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941993	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968236	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1849856	chr3:17646794-17748688	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1828838	chr3:17646794-17757960	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17650800-17681200	Weak transcription	Aorta	Aorta
2	chr3:17656000-17681200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:17657800-17681200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:17660400-17679800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:17664000-17679000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:17664800-17688600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:17664800-17689000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:17668600-17679400	Weak transcription	GM12878-XiMat	blood
9	chr3:17668600-17679600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:17668800-17706200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:17673400-17680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:17673400-17681200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:17674000-17690800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:17674200-17681000	Weak transcription	HSMMtube	muscle
15	chr3:17674200-17687600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:17674400-17679400	Weak transcription	NHLF	lung
17	chr3:17674400-17680800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:17674600-17679200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:17674600-17679800	Weak transcription	NHEK	skin
20	chr3:17674800-17679200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:17674800-17680000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:17675000-17679200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:17677200-17679200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:17677200-17679800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:17677200-17680000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:17677200-17681000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:17677400-17679400	Weak transcription	Osteobl	bone
28	chr3:17677400-17679600	Weak transcription	HSMM	muscle
29	chr3:17677400-17681000	Weak transcription	K562	blood
30	chr3:17677400-17681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:17677600-17679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:17677600-17681000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:17677600-17681200	Weak transcription	Left Ventricle	heart
34	chr3:17677600-17681200	Weak transcription	Right Atrium	heart
35	chr3:17677600-17686800	Weak transcription	Small Intestine	intestine
36	chr3:17677800-17679200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:17677800-17679800	Weak transcription	HUVEC	blood vessel
38	chr3:17677800-17680000	Weak transcription	NH-A	brain
39	chr3:17678000-17679000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:17678000-17679000	Weak transcription	A549	lung
41	chr3:17678000-17679200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:17678000-17679200	Weak transcription	NHDF-Ad	bronchial
43	chr3:17678000-17679600	Weak transcription	Hela-S3	cervix
44	chr3:17678000-17679800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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