Variant report

Variant	rs12054516
Chromosome Location	chr4:7498246-7498247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10027474	1.00[CEU][hapmap]
rs10937830	1.00[GIH][hapmap]
rs11729654	1.00[CEU][hapmap]
rs12054603	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12641162	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12649503	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13114663	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13114671	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4377593	1.00[CEU][hapmap]
rs4563497	1.00[CEU][hapmap]
rs4689129	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4689761	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4689763	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4689764	0.80[AFR][1000 genomes]
rs6813094	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6818189	0.97[AFR][1000 genomes]
rs6818395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9647414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9647418	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv469758	chr4:7370083-7546250	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878561	chr4:7402284-7544610	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878563	chr4:7420785-7529367	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878564	chr4:7421007-7535214	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878566	chr4:7456717-7529367	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
10	nsv878567	chr4:7456717-7544610	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
11	esv34002	chr4:7481398-7508494	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	nsv878568	chr4:7490246-7529367	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3468132	chr4:7496536-7499850	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3412982	chr4:7496543-7499995	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	diseases
15	esv3348889	chr4:7496576-7499872	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv3468131	chr4:7496591-7499849	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
17	esv7927	chr4:7496613-7499803	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
18	esv3499766	chr4:7496613-7499887	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
19	esv3499767	chr4:7496636-7499711	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
20	esv3468133	chr4:7496638-7499711	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
21	nsv878569	chr4:7496857-7544610	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7490200-7498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:7497600-7500800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:7497600-7501000	Weak transcription	Brain Anterior Caudate	brain
4	chr4:7497600-7501000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:7497800-7498800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr4:7497800-7501200	Weak transcription	Brain Substantia Nigra	brain
7	chr4:7498000-7500200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:7498200-7499200	Enhancers	Brain Germinal Matrix	brain

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