Variant report

Variant	rs12500159
Chromosome Location	chr4:79322383-79322384
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12508660	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12512164	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484326	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17003174	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17426103	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17460388	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872266	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975043	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55670221	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55866514	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55945606	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61339663	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810930	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819661	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846299	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72657085	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72657093	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72657094	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7656704	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7671858	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7675357	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7677133	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7677395	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7694602	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869348	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869350	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923018	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12500159	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
2	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79302400-79353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:79309000-79331000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:79309200-79334800	Weak transcription	Fetal Heart	heart
6	chr4:79310000-79330800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:79311000-79334600	Weak transcription	Fetal Lung	lung
8	chr4:79318400-79328200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:79318800-79353600	Weak transcription	Pancreas	Pancrea
10	chr4:79319000-79334000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:79319000-79334000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:79319000-79334200	Weak transcription	Fetal Intestine Large	intestine
13	chr4:79319000-79336000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:79319600-79334400	Weak transcription	Fetal Kidney	kidney
15	chr4:79320000-79400200	Weak transcription	Psoas Muscle	Psoas
16	chr4:79320800-79322800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:79320800-79325400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:79320800-79331400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:79321600-79325000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:79321800-79322800	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr4:79321800-79322800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:79321800-79322800	Strong transcription	HepG2	liver
23	chr4:79321800-79324800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:79321800-79325800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:79321800-79337800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:79322000-79323200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:79322200-79325000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:79322200-79334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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