Variant report

Variant	rs12948266
Chromosome Location	chr17:15421535-15421536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:74032040..74034358-chr17:15420239..15421739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168209	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10153259	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12450262	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450302	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450921	0.85[ASN][1000 genomes]
rs12451284	0.82[ASN][1000 genomes]
rs12452965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453117	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12938444	1.00[ASN][1000 genomes]
rs12939314	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12943480	1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs12953212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940991	1.00[JPT][hapmap]
rs16951395	1.00[ASW][hapmap]
rs17702522	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];1.00[ASN][1000 genomes]
rs17702771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17775544	0.83[AMR][1000 genomes]
rs2013835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2654261	1.00[JPT][hapmap]
rs34236889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34358805	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34453320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34818581	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35078459	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35406616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35448233	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35699886	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097878	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3852809	0.83[ASN][1000 genomes]
rs3911955	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4054418	1.00[JPT][hapmap]
rs4791625	0.83[ASN][1000 genomes]
rs4792619	0.87[ASN][1000 genomes]
rs6502459	0.83[ASN][1000 genomes]
rs6502461	1.00[JPT][hapmap]
rs67294543	0.86[ASN][1000 genomes]
rs71367505	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71367507	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs716388	1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7359511	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8068610	0.85[ASN][1000 genomes]
rs8070714	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8071082	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8074456	1.00[JPT][hapmap]
rs917567	1.00[JPT][hapmap];0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12948266	CDRT4	cis	parietal	SCAN
rs12948266	TEKT3	cis	cerebellum	SCAN
rs12948266	TEKT3	cis	parietal	SCAN
rs12948266	CDRT4	cis	cerebellum	SCAN
rs12948266	PMP22	cis	multi-tissue	Pritchard
rs12948266	TRIM16	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr17:15406600-15422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:15406800-15421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:15406800-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:15407000-15422400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr17:15410200-15426200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:15410800-15429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:15413800-15428000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:15414000-15429000	Weak transcription	Fetal Heart	heart
14	chr17:15414000-15430200	Weak transcription	Right Ventricle	heart
15	chr17:15414600-15422200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:15414600-15428000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr17:15415200-15422400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:15415200-15422600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:15415400-15422400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:15416400-15421800	Strong transcription	Hela-S3	cervix
22	chr17:15417000-15422000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:15417000-15422200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr17:15417400-15421600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:15417400-15422000	Strong transcription	Primary T cells from cord blood	blood
26	chr17:15417400-15422200	Weak transcription	Small Intestine	intestine
27	chr17:15417600-15427200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:15417600-15466400	Weak transcription	Ovary	ovary
29	chr17:15417800-15428200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:15418000-15429200	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:15418200-15421800	Strong transcription	HSMMtube	muscle
32	chr17:15418200-15423000	Strong transcription	Fetal Stomach	stomach
33	chr17:15418400-15422400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:15418400-15422800	Strong transcription	Fetal Intestine Small	intestine
35	chr17:15418400-15430000	Weak transcription	K562	blood
36	chr17:15418400-15430200	Weak transcription	Pancreas	Pancrea
37	chr17:15418600-15429600	Weak transcription	Brain Substantia Nigra	brain
38	chr17:15418600-15450600	Weak transcription	Brain Angular Gyrus	brain
39	chr17:15418800-15422400	Strong transcription	HepG2	liver
40	chr17:15418800-15450600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:15419000-15422000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:15419000-15422400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:15419000-15422400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr17:15419200-15422400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:15419200-15422400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:15419400-15421600	Weak transcription	Esophagus	oesophagus
47	chr17:15419600-15422600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:15419600-15425000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr17:15419600-15442000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:15419800-15425600	Weak transcription	Fetal Intestine Large	intestine

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