Variant report

Variant	rs60567238
Chromosome Location	chr3:51301578-51301579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12485331	0.84[EUR][1000 genomes]
rs12485754	0.84[EUR][1000 genomes]
rs12487468	0.87[AMR][1000 genomes]
rs12487496	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12489219	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490026	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12491836	0.89[EUR][1000 genomes]
rs12492615	0.89[EUR][1000 genomes]
rs12492690	0.89[EUR][1000 genomes]
rs12493034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493323	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493978	0.82[AMR][1000 genomes]
rs12495561	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496830	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1809388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1842394	0.88[AMR][1000 genomes]
rs2086395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101056	0.98[ASN][1000 genomes]
rs2127654	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170177	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2355946	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762711	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4130473	0.89[EUR][1000 genomes]
rs4346580	0.89[EUR][1000 genomes]
rs4468966	0.83[AMR][1000 genomes]
rs4927961	0.89[EUR][1000 genomes]
rs4974100	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974112	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56052360	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57406588	0.89[EUR][1000 genomes]
rs58201844	0.83[AMR][1000 genomes]
rs58911602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59129045	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59682667	0.89[EUR][1000 genomes]
rs59834534	0.89[EUR][1000 genomes]
rs60128296	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60461297	0.89[EUR][1000 genomes]
rs60740654	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61660900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792254	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72936442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72936462	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72941919	0.89[EUR][1000 genomes]
rs72943166	0.89[EUR][1000 genomes]
rs72948197	0.89[EUR][1000 genomes]
rs72948200	0.89[EUR][1000 genomes]
rs72953143	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953162	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953175	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751076	0.84[AMR][1000 genomes]
rs880478	0.84[AMR][1000 genomes]
rs9817077	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9817872	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9819195	0.83[AMR][1000 genomes]
rs9829057	0.83[AMR][1000 genomes]
rs9856134	0.83[AMR][1000 genomes]
rs9878592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
2	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:51285400-51308200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:51295600-51310800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:51296400-51318800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:51297000-51317400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:51297600-51304000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:51298000-51314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:51298400-51319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:51299400-51307200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:51299400-51307800	Weak transcription	Fetal Brain Female	brain
14	chr3:51299600-51307000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:51299800-51307800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:51301400-51301600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:51301400-51301600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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