Variant report

Variant	rs2289333
Chromosome Location	chr15:40617209-40617210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40617173-40617271	MCF10A-Er-Src	breast:	n/a	n/a
2	MAZ	chr15:40614373-40617806	IMR90	lung:	n/a	chr15:40614503-40614513 chr15:40617461-40617470
3	STAT3	chr15:40617062-40617220	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40615499..40617257-chr15:40732436..40735160,2	K562	blood:
2	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
3	chr15:40616209..40618065-chr15:40641977..40644316,2	MCF-7	breast:
4	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:
5	chr15:40573791..40575924-chr15:40613554..40617283,3	MCF-7	breast:
6	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
7	chr15:40599147..40601689-chr15:40614013..40619011,4	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHGR1-1	chr15:40616681-40618914	NONHSAT041825
2	lnc-PHGR1-1	chr15:40616696-40617689	NONHSAT041826
3	lnc-PHGR1-1	chr15:40617141-40618903	l_1150_chr15:40617140-40621361_brain

No data

Variant related genes	Relation type
LINC00984	TF binding region
ENSG00000252714	Chromatin interaction
ENSG00000233041	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000188549	Chromatin interaction
ENSG00000230778	Chromatin interaction
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1077476	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118961	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2289334	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334271	0.95[JPT][hapmap]
rs4923863	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4923864	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924455	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7164564	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164747	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs748245	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs882829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs934937	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3378883	chr15:40614885-40617433	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3428901	chr15:40615210-40617508	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3438791	chr15:40615285-40617833	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289333	C15orf52	cis	cerebellum	SCAN
rs2289333	DISP2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40614800-40618200	Active TSS	Colon Smooth Muscle	Colon
2	chr15:40614800-40618400	Active TSS	Aorta	Aorta
3	chr15:40615200-40617800	Active TSS	Right Atrium	heart
4	chr15:40615400-40617600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:40615400-40617600	Active TSS	Left Ventricle	heart
6	chr15:40615400-40618000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:40615400-40618400	Active TSS	Right Ventricle	heart
8	chr15:40615600-40617400	Active TSS	Pancreas	Pancrea
9	chr15:40615600-40617800	Active TSS	Ovary	ovary
10	chr15:40615800-40618000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr15:40616200-40617400	Active TSS	GM12878-XiMat	blood
12	chr15:40616400-40617400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr15:40616400-40618200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:40616400-40618800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr15:40616600-40617400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr15:40616600-40617400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr15:40616600-40617600	Flanking Active TSS	Colonic Mucosa	Colon
18	chr15:40616600-40617600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr15:40616600-40617600	Flanking Active TSS	Placenta	Placenta
20	chr15:40616600-40617800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:40616600-40618000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr15:40616800-40617400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:40616800-40617400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr15:40616800-40617400	Active TSS	Fetal Heart	heart
25	chr15:40616800-40617400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
26	chr15:40616800-40617400	Flanking Active TSS	Fetal Lung	lung
27	chr15:40616800-40617400	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr15:40616800-40617400	Flanking Active TSS	HepG2	liver
29	chr15:40616800-40617600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:40616800-40617600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr15:40616800-40617600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr15:40616800-40617600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:40616800-40617600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr15:40616800-40617600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr15:40616800-40617600	Flanking Active TSS	Psoas Muscle	Psoas
36	chr15:40616800-40617800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:40616800-40618000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr15:40616800-40618000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:40616800-40618000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr15:40616800-40618200	Flanking Active TSS	HUVEC	blood vessel
41	chr15:40616800-40618400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr15:40616800-40618400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr15:40617000-40617400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:40617000-40617400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:40617000-40617400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:40617000-40617400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:40617000-40617400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr15:40617000-40617400	Flanking Active TSS	Fetal Brain Male	brain
49	chr15:40617000-40617400	Flanking Active TSS	Fetal Kidney	kidney
50	chr15:40617000-40617400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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