Variant report

Variant	rs2052022
Chromosome Location	chr17:15404987-15404988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:15393755..15395378-chr17:15403232..15405420,2	MCF-7	breast:
2	chr17:15398558..15401467-chr17:15403715..15406504,4	K562	blood:
3	chr17:15398558..15401467-chr17:15404011..15406504,2	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	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11653403	0.81[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1465251	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1465252	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17775352	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs236810	0.82[MKK][hapmap]
rs28411195	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28733269	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2938158	0.81[MKK][hapmap]
rs4572441	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55749051	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62069953	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62072569	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62072571	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62072579	0.82[ASN][1000 genomes]
rs716389	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7211982	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7215138	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8076852	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9899922	0.85[ASN][1000 genomes]
rs9901383	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9903674	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9904986	0.82[CHB][hapmap]
rs9908651	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9911005	0.87[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9911822	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9913509	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.90[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
rs2052022	TEKT3	cis	parietal	SCAN
rs2052022	CDRT4	cis	brain	seeQTL
rs2052022	TEKT3	cis	cerebellum	SCAN
rs2052022	CDRT4	cis	cerebellum	SCAN
rs2052022	CDRT4	cis	parietal	SCAN
rs2052022	PMP22	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr17:15369200-15405000	Weak transcription	Esophagus	oesophagus
3	chr17:15377400-15406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
5	chr17:15383400-15455000	Weak transcription	Gastric	stomach
6	chr17:15383800-15405200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:15383800-15406000	Weak transcription	NHEK	skin
8	chr17:15384600-15406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
10	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
11	chr17:15387400-15405000	Weak transcription	Lung	lung
12	chr17:15388600-15406000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:15393000-15406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:15393800-15405400	Weak transcription	Colonic Mucosa	Colon
16	chr17:15394400-15405800	Weak transcription	Aorta	Aorta
17	chr17:15394400-15406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:15394600-15405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:15394600-15405000	Weak transcription	Fetal Lung	lung
20	chr17:15394600-15405000	Weak transcription	Spleen	Spleen
21	chr17:15394600-15405200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:15394600-15405200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr17:15394600-15405600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:15394600-15406400	Weak transcription	Stomach Mucosa	stomach
25	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr17:15394800-15405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:15395000-15405400	Weak transcription	NHLF	lung
29	chr17:15395000-15405600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:15395000-15410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:15395400-15405200	Weak transcription	Brain Angular Gyrus	brain
32	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
33	chr17:15395800-15405800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
35	chr17:15396400-15405200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:15396600-15405800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:15396800-15405000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:15396800-15405000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:15396800-15405000	Weak transcription	Fetal Muscle Leg	muscle
40	chr17:15396800-15405200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr17:15397000-15405000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:15397000-15405200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:15397000-15405400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:15397000-15406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr17:15397200-15405400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:15397400-15405400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:15397800-15405200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:15398000-15405200	Strong transcription	Osteobl	bone
50	chr17:15398000-15406200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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