Variant report

Variant	rs7211982
Chromosome Location	chr17:15394372-15394373
allele	C/T
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: 35 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11651787	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11653403	0.96[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs1465251	0.96[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs1465252	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2052022	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs236810	0.85[LWK][hapmap];0.93[MKK][hapmap]
rs28411195	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28733269	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2938158	0.83[LWK][hapmap];0.92[MKK][hapmap]
rs3865257	0.80[EUR][1000 genomes]
rs4572441	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55749051	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62069953	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62072569	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62072571	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62072578	0.83[EUR][1000 genomes]
rs716389	1.00[ASW][hapmap];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7215138	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8076852	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9899922	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903674	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9904986	0.82[CHB][hapmap]
rs9908651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9911005	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9911822	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9913509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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
rs7211982	PMP22	cis	multi-tissue	Pritchard
rs7211982	CDRT4	cis	parietal	SCAN
rs7211982	TEKT3	cis	parietal	SCAN
rs7211982	CDRT4	cis	brain	seeQTL
rs7211982	TEKT3	cis	cerebellum	SCAN
rs7211982	CDRT4	cis	cerebellum	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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