Variant report

Variant	rs12453117
Chromosome Location	chr17:15394395-15394396
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:15393209..15396185-chr17:15400258..15402130,2	MCF-7	breast:
2	chr17:15393755..15395378-chr17:15403232..15405420,2	MCF-7	breast:
3	chr17:15392637..15397367-chr17:15398758..15404412,8	K562	blood:
4	chr17:13269628..13272231-chr17:15394003..15396327,2	MCF-7	breast:
5	chr17:15392701..15397152-chr17:15398701..15402500,5	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10153259	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs12450262	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12450302	0.95[ASN][1000 genomes]
rs12450921	0.81[ASN][1000 genomes]
rs12452965	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12453059	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12938444	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12939314	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12943480	1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs12948266	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12953212	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16940991	1.00[JPT][hapmap]
rs17702522	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17702771	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2013835	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2654261	1.00[JPT][hapmap]
rs34236889	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34358805	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34453320	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34818581	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35078459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35406616	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35448233	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35699886	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs36097878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911955	1.00[JPT][hapmap]
rs4054418	1.00[JPT][hapmap]
rs4792619	0.83[ASN][1000 genomes]
rs6502461	1.00[JPT][hapmap]
rs67294543	0.82[ASN][1000 genomes]
rs71367505	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71367507	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs716388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7359511	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8068610	0.81[ASN][1000 genomes]
rs8070714	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8071082	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8074456	1.00[JPT][hapmap]
rs917567	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12453117	TEKT3	cis	parietal	SCAN
rs12453117	CDRT4	cis	cerebellum	SCAN
rs12453117	SNORD49B	cis	parietal	SCAN
rs12453117	TEKT3	cis	cerebellum	SCAN
rs12453117	TRIM16	cis	parietal	SCAN
rs12453117	CDRT4	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
3	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr17:15369000-15401600	Weak transcription	Brain Germinal Matrix	brain
5	chr17:15369200-15405000	Weak transcription	Esophagus	oesophagus
6	chr17:15377400-15406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr17:15382800-15394400	Weak transcription	Spleen	Spleen
8	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
9	chr17:15383400-15402200	Weak transcription	A549	lung
10	chr17:15383400-15455000	Weak transcription	Gastric	stomach
11	chr17:15383600-15395800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:15383800-15398400	Weak transcription	Fetal Kidney	kidney
13	chr17:15383800-15401400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:15383800-15405200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:15383800-15406000	Weak transcription	NHEK	skin
16	chr17:15384600-15406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:15385400-15395800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
19	chr17:15387200-15400000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:15387200-15403800	Weak transcription	Liver	Liver
21	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
22	chr17:15387400-15399400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr17:15387400-15405000	Weak transcription	Lung	lung
24	chr17:15388000-15401600	Weak transcription	Ovary	ovary
25	chr17:15388600-15406000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr17:15389800-15398800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:15390000-15397200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:15390600-15396800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr17:15391800-15399000	Weak transcription	HepG2	liver
30	chr17:15392200-15395400	Enhancers	Left Ventricle	heart
31	chr17:15392600-15394400	Weak transcription	Fetal Lung	lung
32	chr17:15393000-15406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:15393200-15395600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:15393400-15394400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:15393400-15394600	Enhancers	Placenta	Placenta
36	chr17:15393400-15395800	Enhancers	HUVEC	blood vessel
37	chr17:15393400-15396800	Enhancers	Fetal Muscle Leg	muscle
38	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr17:15393600-15394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:15393600-15394400	Strong transcription	Aorta	Aorta
41	chr17:15393600-15394400	Genic enhancers	Fetal Stomach	stomach
42	chr17:15393600-15394600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:15393600-15394600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr17:15393600-15394600	Enhancers	Primary hematopoietic stem cells	blood
45	chr17:15393600-15394600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:15393600-15394600	Enhancers	Fetal Muscle Trunk	muscle
47	chr17:15393600-15394600	Enhancers	Right Atrium	heart
48	chr17:15393600-15394600	Enhancers	HSMM	muscle
49	chr17:15393600-15394800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:15393600-15394800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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