Variant report

Variant	rs17158267
Chromosome Location	chr15:83497589-83497590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83378862..83381200-chr15:83497149..83499463,2	K562	blood:
2	chr15:83497018..83500985-chr15:83502247..83506806,4	MCF-7	breast:
3	chr15:83495845..83498669-chr15:83504409..83507025,2	K562	blood:
4	chr15:83477460..83480587-chr15:83496112..83502372,6	K562	blood:

Variant related genes	Relation type
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1108135	0.80[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11259954	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[AMR][1000 genomes]
rs12592976	0.80[CEU][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs17158194	0.87[MKK][hapmap]
rs17158253	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17158257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158366	0.84[GIH][hapmap];0.81[MEX][hapmap]
rs17841165	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306428	0.82[MKK][hapmap]
rs28698473	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55994896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56108482	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57612574	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58229275	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs60686632	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66978683	0.83[EUR][1000 genomes]
rs73443061	0.81[EUR][1000 genomes]
rs8036227	0.92[GIH][hapmap];0.81[MEX][hapmap]
rs899747	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv977748	chr15:83496161-83500241	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17158267	WHAMM	cis	brain	seeQTL
rs17158267	ST20	cis	cerebellum	SCAN
rs17158267	C20orf103	trans	lymphoblastoid	seeQTL
rs17158267	SCAND2	cis	cerebellum	SCAN
rs17158267	KIAA1971	cis	multi-tissue	Pritchard
rs17158267	WHAMM	trans	brain	seeQTL
rs17158267	CIB2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
5	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:83481000-83499800	Weak transcription	Fetal Heart	heart
7	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:83481400-83500800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:83481400-83507000	Strong transcription	Placenta	Placenta
10	chr15:83481600-83500800	Strong transcription	Fetal Thymus	thymus
11	chr15:83481600-83507000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:83481800-83499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:83481800-83500000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:83481800-83506200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:83481800-83507000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
17	chr15:83482000-83500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:83482000-83500200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:83482000-83506800	Strong transcription	Fetal Intestine Large	intestine
20	chr15:83482000-83507000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:83482200-83500200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:83482200-83507000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr15:83482600-83500200	Strong transcription	Fetal Lung	lung
24	chr15:83482800-83500400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:83482800-83506800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:83483200-83507400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:83484800-83505400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:83485200-83500600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:83485400-83500600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr15:83487800-83500200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:83488400-83505000	Strong transcription	Fetal Stomach	stomach
32	chr15:83488800-83501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:83489200-83500200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:83489200-83500800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:83489200-83506800	Weak transcription	Fetal Brain Male	brain
36	chr15:83489800-83499800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:83491000-83499400	Strong transcription	GM12878-XiMat	blood
38	chr15:83491000-83500600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:83491000-83500600	Strong transcription	HSMM	muscle
40	chr15:83491000-83508000	Strong transcription	Thymus	Thymus
41	chr15:83491200-83499400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:83491200-83506400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr15:83491200-83507400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:83491400-83499200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:83491400-83499400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:83491400-83500200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:83491400-83500200	Strong transcription	NH-A	brain
48	chr15:83491400-83505000	Strong transcription	Spleen	Spleen
49	chr15:83491400-83506600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:83491400-83507400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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