Variant report

Variant	rs1880809
Chromosome Location	chr2:78533899-78533900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1358138	0.86[AFR][1000 genomes]
rs1405273	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1405274	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17015122	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015124	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015126	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015127	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1818965	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1818966	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1997149	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4853379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4853380	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55932665	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56135564	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56300004	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57127297	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57397075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59016424	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59297352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59828838	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59969929	0.99[EUR][1000 genomes]
rs6726120	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6742860	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6743486	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6743622	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72912068	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7577263	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7585321	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7598514	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7601955	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917204	chr2:78047538-78602013	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001461	chr2:78091352-78673948	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757811	chr2:78126389-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759068	chr2:78126389-78711032	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2756933	chr2:78199735-78640246	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524102	chr2:78221253-78562013	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2762686	chr2:78224683-78564328	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv34528	chr2:78256829-78615143	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv818057	chr2:78263883-78633880	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1005115	chr2:78307330-78673948	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1002464	chr2:78308336-78658280	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv535787	chr2:78308336-78658280	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv582270	chr2:78367077-78592167	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1011578	chr2:78368127-78590333	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv874357	chr2:78395467-78546919	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv1010116	chr2:78399683-78660165	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv998161	chr2:78404349-78660165	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1000078	chr2:78410008-78660165	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv428710	chr2:78451500-78602039	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv1008976	chr2:78455070-78541719	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1002114	chr2:78511306-78743191	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv535789	chr2:78511306-78743191	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv1005419	chr2:78511953-78536293	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
29	nsv834271	chr2:78519702-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78529000-78536200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:78531600-78534800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:78532200-78534200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:78532200-78534200	Weak transcription	HepG2	liver
5	chr2:78532200-78535600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:78532200-78536600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:78532600-78534200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:78532800-78534000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:78533200-78534600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:78533600-78534000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:78533600-78534000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:78533600-78534200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:78533600-78536200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:78533800-78534800	Enhancers	HUES64 Cell Line	embryonic stem cell

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