Variant report

Variant	rs12512164
Chromosome Location	chr4:79300993-79300994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12500159	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508660	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1484326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003169	0.87[ASW][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17003174	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17426103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17460388	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975043	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55670221	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55866514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61339663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810930	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6819661	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846299	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72657085	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72657093	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72657094	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7656704	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7675357	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677133	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677395	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694602	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869350	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3443485	chr4:79300628-79303526	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12512164	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79275400-79310600	Weak transcription	Aorta	Aorta
2	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
3	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
4	chr4:79290200-79310800	Weak transcription	Brain Anterior Caudate	brain
5	chr4:79291200-79308400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:79291200-79314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:79291800-79301400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:79291800-79306400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:79291800-79307200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:79291800-79318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:79292000-79312000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr4:79292200-79301000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:79292200-79306600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:79292200-79308400	Weak transcription	Fetal Lung	lung
15	chr4:79292200-79312200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:79292400-79310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:79292400-79312000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:79292600-79301200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:79295400-79301800	Weak transcription	Psoas Muscle	Psoas
20	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:79297000-79301200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:79297600-79301800	Weak transcription	Fetal Kidney	kidney
23	chr4:79297600-79310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:79298000-79308000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:79299400-79302000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:79299400-79308600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:79299800-79301000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:79300200-79301200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:79300200-79301200	Enhancers	NHDF-Ad	bronchial
30	chr4:79300200-79302000	Enhancers	NHEK	skin
31	chr4:79300200-79302400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:79300200-79302400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:79300200-79302400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:79300400-79301200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:79300400-79301800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:79300400-79302200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:79300400-79302400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:79300400-79302400	Enhancers	HMEC	breast
39	chr4:79300400-79303000	Strong transcription	HepG2	liver
40	chr4:79300600-79301000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr4:79300600-79302200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr4:79300800-79301000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr4:79300800-79301200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr4:79300800-79301200	Weak transcription	HSMMtube	muscle
45	chr4:79300800-79301800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:79300800-79302000	Enhancers	Fetal Intestine Small	intestine
47	chr4:79300800-79302400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:79300800-79302400	Enhancers	Fetal Heart	heart
49	chr4:79300800-79313200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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