Variant report

Variant	rs1062229
Chromosome Location	chr14:25489283-25489284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10483295	1.00[ASN][1000 genomes]
rs11626966	1.00[CHB][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11627467	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627899	0.81[EUR][1000 genomes]
rs11628114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs17109491	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17109498	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17109521	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17109529	0.84[CEU][hapmap];0.95[EUR][1000 genomes]
rs17109538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs17109542	0.81[EUR][1000 genomes]
rs17795976	0.81[EUR][1000 genomes]
rs17795982	0.81[EUR][1000 genomes]
rs1952501	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2225270	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55660351	0.81[EUR][1000 genomes]
rs72682999	1.00[ASN][1000 genomes]
rs8004569	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8004614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv901510	chr14:25476170-25526309	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1062229	AP1G2	cis	cerebellum	SCAN
rs1062229	CEBPE	cis	parietal	SCAN
rs1062229	SLC7A7	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25479400-25508600	Weak transcription	Brain Anterior Caudate	brain
2	chr14:25479600-25494800	Weak transcription	Stomach Mucosa	stomach
3	chr14:25479800-25501000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:25480000-25490000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:25480000-25490000	Weak transcription	Right Atrium	heart
6	chr14:25481200-25507400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr14:25485200-25501600	Weak transcription	Fetal Intestine Small	intestine
8	chr14:25485400-25493600	Weak transcription	Fetal Lung	lung
9	chr14:25487600-25489800	Weak transcription	Left Ventricle	heart
10	chr14:25488000-25489800	Weak transcription	Right Ventricle	heart
11	chr14:25488000-25505000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:25488200-25489800	Weak transcription	Aorta	Aorta
13	chr14:25488200-25490400	Enhancers	Fetal Brain Male	brain
14	chr14:25489200-25490000	Enhancers	Fetal Brain Female	brain
15	chr14:25489200-25490600	Enhancers	Pancreas	Pancrea

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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