Variant report

Variant	rs11070279
Chromosome Location	chr15:40860946-40860947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:40860597-40862522	SK-N-SH	brain:	n/a	n/a
2	MAX	chr15:40860862-40861123	K562	blood:	n/a	n/a
3	MTA3	chr15:40860783-40861623	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:40860888-40862953	PFSK-1	brain:	n/a	n/a
5	CTCF	chr15:40860840-40860990	HRE	kidney:	n/a	n/a
6	POLR2A	chr15:40860911-40863037	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr15:40860914-40861003	K562	blood:	n/a	n/a
8	HCFC1	chr15:40860574-40863139	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:40860936-40861978	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40860821..40863087-chr15:40987318..40989233,3	K562	blood:

Variant related genes	Relation type
C15orf57	TF binding region
RPUSD2	TF binding region
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1051482	0.96[CEU][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10851396	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070280	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852479	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855517	0.82[EUR][1000 genomes]
rs11857247	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148185	0.96[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs12899408	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906755	0.86[EUR][1000 genomes]
rs12907448	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907984	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908114	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908443	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12914501	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915563	0.87[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12916323	0.91[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1453183	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]
rs17746659	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747399	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2123534	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2304583	0.87[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs2412545	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs28798094	0.82[EUR][1000 genomes]
rs3213999	0.83[CEU][hapmap]
rs34303240	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34750756	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35884042	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36094699	0.82[EUR][1000 genomes]
rs36122190	0.80[AMR][1000 genomes]
rs3743146	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803353	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4457966	0.95[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5030783	0.87[CEU][hapmap]
rs55954396	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56384845	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61048252	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018046	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62018048	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018051	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62019866	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62019883	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62019934	0.81[EUR][1000 genomes]
rs7162749	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164385	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165054	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181909	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72733469	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731640	0.80[EUR][1000 genomes]
rs733299	0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs8025458	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8028910	0.92[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036938	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8038396	0.87[EUR][1000 genomes]
rs8042733	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672313	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs9806410	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972363	0.88[MEX][hapmap]
rs999197	0.92[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
rs11070279	LPCAT4	cis	parietal	SCAN
rs11070279	C15orf57	cis	cerebellum	SCAN
rs11070279	RP11-111A22.1	cis	Stomach	GTEx
rs11070279	C15orf57	cis	parietal	SCAN
rs11070279	ZFYVE19	cis	parietal	SCAN
rs11070279	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs11070279	C15orf57	cis	lung	GTEx
rs11070279	CCDC32	cis	multi-tissue	Pritchard
rs11070279	ZFYVE19	cis	multi-tissue	Pritchard
rs11070279	MGC20481	cis	multi-tissue	Pritchard
rs11070279	MRPL42P5	cis	multi-tissue	Pritchard
rs11070279	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs11070279	ZFYVE19	cis	cerebellum	SCAN
rs11070279	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs11070279	C15orf57	cis	Artery Tibial	GTEx
rs11070279	C15orf57	cis	Lymphoblastoid	GTEx
rs11070279	C15orf57	cis	Stomach	GTEx
rs11070279	C15orf57	cis	Cerebellum	GTEx
rs11070279	RP11-111A22.1	cis	lung	GTEx
rs11070279	PLA2G4E	cis	parietal	SCAN
rs11070279	RP11-111A22.1	cis	Artery Aorta	GTEx
rs11070279	ITPKA	cis	parietal	SCAN
rs11070279	C15orf57	cis	Esophagus Muscularis	GTEx
rs11070279	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11070279	C15orf23	cis	cerebellum	SCAN
rs11070279	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs11070279	C15orf57	cis	Nerve Tibial	GTEx
rs11070279	C15orf57	cis	Artery Aorta	GTEx
rs11070279	C15orf57	cis	Esophagus Mucosa	GTEx
rs11070279	C15orf57	cis	Adipose Subcutaneous	GTEx
rs11070279	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs11070279	IVD	cis	cerebellum	SCAN
rs11070279	C15orf57	cis	lymphoblastoid	seeQTL
rs11070279	CCDC32	cis	lesional skin	skin_eQTL
rs11070279	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40857800-40861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:40857800-40861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:40857800-40861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40857800-40861000	Weak transcription	HSMM	muscle
6	chr15:40857800-40861000	Weak transcription	HSMMtube	muscle
7	chr15:40857800-40861200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:40857800-40861200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:40858000-40861000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:40858000-40861000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:40858000-40861000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:40858000-40861000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:40858000-40861000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:40858000-40861000	Weak transcription	Right Ventricle	heart
15	chr15:40858000-40861200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:40858000-40861200	Weak transcription	Lung	lung
17	chr15:40858000-40861200	Weak transcription	Pancreas	Pancrea
18	chr15:40858000-40861400	Weak transcription	Spleen	Spleen
19	chr15:40858200-40861000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:40859600-40861000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:40859800-40861000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:40860400-40861000	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:40860600-40861000	Enhancers	Primary T cells from cord blood	blood
24	chr15:40860600-40861000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr15:40860600-40861000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:40860600-40861000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:40860600-40861000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:40860600-40861000	Enhancers	Liver	Liver
29	chr15:40860600-40861000	Enhancers	Brain Germinal Matrix	brain
30	chr15:40860600-40861000	Enhancers	Fetal Intestine Large	intestine
31	chr15:40860600-40861000	Enhancers	Fetal Muscle Leg	muscle
32	chr15:40860600-40861000	Enhancers	Stomach Smooth Muscle	stomach
33	chr15:40860600-40861000	Flanking Active TSS	HepG2	liver
34	chr15:40860600-40861200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:40860600-40861200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:40860600-40861200	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr15:40860600-40861200	Flanking Active TSS	Hela-S3	cervix
38	chr15:40860600-40862200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:40860800-40861000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:40860800-40861000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:40860800-40861000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr15:40860800-40861000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr15:40860800-40861000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr15:40860800-40861000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr15:40860800-40861000	Enhancers	Primary hematopoietic stem cells	blood
46	chr15:40860800-40861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:40860800-40861000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:40860800-40861000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr15:40860800-40861000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:40860800-40861000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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