Variant report

Variant	rs1453183
Chromosome Location	chr15:40862930-40862931
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	chr15:40855657..40859262-chr15:40860971..40863634,5	MCF-7	breast:
2	chr15:40860821..40863087-chr15:40987318..40989233,3	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1051482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10851396	1.00[ASW][hapmap];0.96[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070279	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070280	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852479	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855517	0.81[EUR][1000 genomes]
rs11857247	0.96[CEU][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12148185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs12898552	0.84[CHB][hapmap]
rs12899408	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12906755	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12907448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12907984	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12908114	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12908443	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908867	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12915563	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916323	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17746659	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17747399	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2123534	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2304583	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs2412545	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs28798094	0.83[EUR][1000 genomes]
rs3213999	0.87[CEU][hapmap]
rs34303240	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34750756	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35030447	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35884042	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36094699	0.82[EUR][1000 genomes]
rs36122190	0.82[AMR][1000 genomes]
rs3743146	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3803353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4457966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5030783	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs55954396	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56384845	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61048252	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018030	0.80[EUR][1000 genomes]
rs62018046	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62018048	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018051	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62019866	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62019883	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62019934	0.81[EUR][1000 genomes]
rs7162749	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7164385	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7165054	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181909	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72733469	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731640	0.83[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs733299	0.83[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs8025458	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8028910	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036938	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8038396	0.86[EUR][1000 genomes]
rs8042733	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9672313	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs9806410	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9972363	0.88[MEX][hapmap]
rs999197	0.96[CEU][hapmap]

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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs1453183	IVD	cis	cerebellum	SCAN
rs1453183	C15orf57	cis	Artery Tibial	GTEx
rs1453183	C15orf57	cis	Nerve Tibial	GTEx
rs1453183	C15orf57	cis	Esophagus Muscularis	GTEx
rs1453183	ZFYVE19	cis	multi-tissue	Pritchard
rs1453183	RP11-111A22.1	cis	Artery Aorta	GTEx
rs1453183	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs1453183	ZFYVE19	cis	parietal	SCAN
rs1453183	CCDC32	cis	multi-tissue	Pritchard
rs1453183	RP11-111A22.1	cis	Stomach	GTEx
rs1453183	C15orf57	cis	Muscle Skeletal	GTEx
rs1453183	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs1453183	C15orf57	cis	cerebellum	SCAN
rs1453183	RP11-111A22.1	cis	lung	GTEx
rs1453183	C15orf57	cis	Stomach	GTEx
rs1453183	ZFYVE19	cis	cerebellum	SCAN
rs1453183	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs1453183	C15orf57	cis	Adipose Subcutaneous	GTEx
rs1453183	MGC20481	cis	multi-tissue	Pritchard
rs1453183	LPCAT4	cis	parietal	SCAN
rs1453183	RP11-111A22.1	cis	Artery Tibial	GTEx
rs1453183	C15orf57	cis	lung	GTEx
rs1453183	C15orf57	cis	Esophagus Mucosa	GTEx
rs1453183	ITPKA	cis	parietal	SCAN
rs1453183	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs1453183	MRPL42P5	cis	multi-tissue	Pritchard
rs1453183	C15orf57	cis	Cerebellum	GTEx
rs1453183	C15orf57	cis	lymphoblastoid	seeQTL
rs1453183	C15orf57	cis	parietal	SCAN
rs1453183	C15orf23	cis	cerebellum	SCAN
rs1453183	CCDC32	cis	lesional skin	skin_eQTL
rs1453183	C15orf57	cis	Artery Aorta	GTEx
rs1453183	PLA2G4E	cis	parietal	SCAN
rs1453183	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs1453183	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40860800-40863200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:40861000-40863000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr15:40861000-40863000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:40861000-40863200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40861800-40863000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr15:40862000-40863000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr15:40862000-40863200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr15:40862000-40863200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:40862200-40863000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:40862200-40863000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:40862200-40863000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr15:40862200-40863000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr15:40862200-40863000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr15:40862200-40863000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr15:40862200-40863000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr15:40862200-40863000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:40862200-40863000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:40862200-40863000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40862200-40863000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr15:40862200-40863000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr15:40862200-40863000	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr15:40862200-40863000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr15:40862200-40863000	Flanking Active TSS	Fetal Brain Female	brain
24	chr15:40862200-40863000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr15:40862200-40863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr15:40862200-40863000	Flanking Active TSS	Osteobl	bone
27	chr15:40862200-40863200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:40862200-40863200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr15:40862200-40863200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:40862200-40863200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:40862200-40863200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr15:40862200-40863200	Flanking Active TSS	Hela-S3	cervix
33	chr15:40862200-40863400	Enhancers	Spleen	Spleen
34	chr15:40862400-40863000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr15:40862400-40863000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:40862400-40863000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr15:40862400-40863000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:40862400-40863000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:40862400-40863000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr15:40862400-40863000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr15:40862400-40863000	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr15:40862400-40863000	Flanking Active TSS	Fetal Kidney	kidney
43	chr15:40862400-40863000	Enhancers	Small Intestine	intestine
44	chr15:40862400-40863000	Flanking Active TSS	A549	lung
45	chr15:40862400-40863000	Flanking Active TSS	HepG2	liver
46	chr15:40862400-40863000	Flanking Active TSS	HMEC	breast
47	chr15:40862400-40863000	Flanking Active TSS	K562	blood
48	chr15:40862400-40863000	Flanking Active TSS	NH-A	brain
49	chr15:40862400-40863000	Flanking Active TSS	NHEK	skin
50	chr15:40862400-40863000	Flanking Active TSS	NHLF	lung

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