Variant report

Variant	rs12450921
Chromosome Location	chr17:15424657-15424658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10153259	0.81[ASN][1000 genomes]
rs12450262	0.85[ASN][1000 genomes]
rs12450302	0.85[ASN][1000 genomes]
rs12451284	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452965	0.81[ASN][1000 genomes]
rs12453117	0.81[ASN][1000 genomes]
rs12938444	0.85[ASN][1000 genomes]
rs12943480	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948266	0.85[ASN][1000 genomes]
rs12953212	0.85[ASN][1000 genomes]
rs17702522	0.85[ASN][1000 genomes]
rs2013835	0.85[ASN][1000 genomes]
rs2532479	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2654261	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34236889	0.85[ASN][1000 genomes]
rs34358805	0.81[ASN][1000 genomes]
rs34453320	0.85[ASN][1000 genomes]
rs34818581	0.81[ASN][1000 genomes]
rs35078459	0.85[ASN][1000 genomes]
rs35406616	0.85[ASN][1000 genomes]
rs35448233	0.85[ASN][1000 genomes]
rs35699886	0.85[ASN][1000 genomes]
rs36097878	0.81[ASN][1000 genomes]
rs3852809	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3911955	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4054418	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4791625	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792619	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502462	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71367505	0.83[ASN][1000 genomes]
rs716388	0.85[ASN][1000 genomes]
rs7226342	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7359507	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8064461	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8068610	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071082	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074456	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917567	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12450921	AC005517.3	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383400-15455000	Weak transcription	Gastric	stomach
2	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:15410200-15426200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:15410800-15429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:15413800-15428000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr17:15414000-15429000	Weak transcription	Fetal Heart	heart
10	chr17:15414000-15430200	Weak transcription	Right Ventricle	heart
11	chr17:15414600-15428000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:15417600-15427200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:15417600-15466400	Weak transcription	Ovary	ovary
15	chr17:15417800-15428200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:15418000-15429200	Weak transcription	Colon Smooth Muscle	Colon
17	chr17:15418400-15430000	Weak transcription	K562	blood
18	chr17:15418400-15430200	Weak transcription	Pancreas	Pancrea
19	chr17:15418600-15429600	Weak transcription	Brain Substantia Nigra	brain
20	chr17:15418600-15450600	Weak transcription	Brain Angular Gyrus	brain
21	chr17:15418800-15450600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:15419600-15425000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:15419600-15442000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr17:15419800-15425600	Weak transcription	Fetal Intestine Large	intestine
25	chr17:15419800-15442400	Weak transcription	Thymus	Thymus
26	chr17:15419800-15448400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:15420000-15425600	Weak transcription	Liver	Liver
28	chr17:15420000-15428200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr17:15420000-15428800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:15420000-15428800	Weak transcription	Fetal Lung	lung
31	chr17:15420000-15429600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:15420000-15429800	Weak transcription	Brain Anterior Caudate	brain
33	chr17:15420000-15441800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr17:15420000-15442000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:15420000-15442000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:15420000-15442000	Weak transcription	A549	lung
37	chr17:15420000-15448400	Weak transcription	Placenta	Placenta
38	chr17:15420000-15450800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:15420200-15428600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:15420200-15442000	Weak transcription	Lung	lung
41	chr17:15420200-15448600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:15420400-15428200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:15420400-15429000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:15420400-15435200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr17:15420400-15442000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:15420400-15442000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr17:15420400-15442000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:15420400-15452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:15420600-15435600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr17:15420600-15441800	Weak transcription	Fetal Brain Female	brain

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