Variant report

Variant	rs60459720
Chromosome Location	chr3:17628911-17628912
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11914537	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11914797	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11915560	0.87[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	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11922861	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923635	0.90[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926072	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926087	1.00[EUR][1000 genomes]
rs11926251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927232	1.00[EUR][1000 genomes]
rs11927283	0.82[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	0.95[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	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12106900	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12107061	1.00[EUR][1000 genomes]
rs12152509	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12185952	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28525383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57352109	1.00[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	0.82[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59960076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60245392	1.00[EUR][1000 genomes]
rs60662240	1.00[EUR][1000 genomes]
rs60803166	1.00[EUR][1000 genomes]
rs60838916	1.00[EUR][1000 genomes]
rs60940413	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61650046	1.00[EUR][1000 genomes]
rs61698855	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577595	1.00[EUR][1000 genomes]
rs6577629	0.91[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]
rs73145898	1.00[EUR][1000 genomes]
rs73156379	1.00[EUR][1000 genomes]
rs73160940	0.87[AMR][1000 genomes]
rs73160942	0.87[AMR][1000 genomes]
rs73160943	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160950	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160951	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160957	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160967	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73161427	1.00[EUR][1000 genomes]
rs73161452	1.00[EUR][1000 genomes]
rs73164768	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165729	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165734	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165735	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165764	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165775	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165777	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165779	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165792	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165798	0.95[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73167510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167513	1.00[EUR][1000 genomes]
rs73167514	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167523	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167527	0.85[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170855	1.00[EUR][1000 genomes]
rs73170858	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170877	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170878	0.82[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	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7620585	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621577	1.00[EUR][1000 genomes]
rs7630381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631803	1.00[EUR][1000 genomes]
rs7648122	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9680896	1.00[EUR][1000 genomes]
rs9754654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9754657	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941993	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968236	1.00[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	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17616000-17663600	Weak transcription	Left Ventricle	heart
2	chr3:17619800-17631600	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:17620000-17631600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:17621600-17629800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:17621600-17631400	Weak transcription	Fetal Thymus	thymus
6	chr3:17622000-17630800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:17622000-17632200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:17622200-17631200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:17622200-17638800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:17622600-17631200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:17622600-17631600	Weak transcription	Primary B cells from cord blood	blood
12	chr3:17622800-17631000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:17623600-17631400	Weak transcription	Fetal Lung	lung
14	chr3:17623800-17631400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:17625400-17633000	Weak transcription	Psoas Muscle	Psoas
16	chr3:17626600-17631600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:17627000-17631800	Weak transcription	Liver	Liver
18	chr3:17627600-17631400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:17627600-17631800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:17627800-17631000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:17627800-17638800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:17628000-17631000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:17628200-17631600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:17628400-17631600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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