Variant report

Variant	rs1077476
Chromosome Location	chr15:40619743-40619744
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40619456..40622052-chr15:40729021..40731269,2	K562	blood:
2	chr15:40618049..40622052-chr15:40729021..40731269,3	K562	blood:
3	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:
4	chr15:40619706..40623827-chr15:40624940..40628910,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHGR1-1	chr15:40619622-40621361	l_1150_chr15:40617140-40621361_brain

Variant related genes	Relation type
ENSG00000252714	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11070264	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12081	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118961	0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes]
rs2289333	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]
rs2289334	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4334271	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4923863	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923864	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164564	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164747	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7173747	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs748245	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs882829	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs934937	0.90[JPT][hapmap];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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1077476	C15orf52	cis	cerebellum	SCAN
rs1077476	DISP2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617000-40622800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40617200-40630200	Weak transcription	A549	lung
3	chr15:40617400-40619800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:40617400-40621800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:40617400-40623000	Enhancers	Fetal Brain Male	brain
6	chr15:40617400-40623800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:40617400-40624000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:40617400-40626000	Weak transcription	Liver	Liver
9	chr15:40617400-40626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:40617400-40626400	Weak transcription	Pancreas	Pancrea
11	chr15:40617400-40627000	Weak transcription	Gastric	stomach
12	chr15:40617600-40620200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:40617600-40620200	Weak transcription	Fetal Kidney	kidney
14	chr15:40617600-40622400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:40617600-40623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr15:40617800-40619800	Weak transcription	Ovary	ovary
17	chr15:40617800-40620000	Weak transcription	Primary T cells from cord blood	blood
18	chr15:40617800-40620000	Genic enhancers	HSMM	muscle
19	chr15:40617800-40620200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:40617800-40620600	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:40617800-40623000	Enhancers	HMEC	breast
22	chr15:40617800-40625000	Weak transcription	Psoas Muscle	Psoas
23	chr15:40618000-40620000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:40618000-40620400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:40618000-40622600	Weak transcription	NHLF	lung
26	chr15:40618000-40624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:40618000-40624400	Enhancers	NHDF-Ad	bronchial
28	chr15:40618000-40625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:40618000-40625800	Weak transcription	Dnd41	blood
30	chr15:40618200-40619800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr15:40618200-40619800	Enhancers	HSMMtube	muscle
32	chr15:40618200-40620200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:40618200-40620400	Genic enhancers	K562	blood
34	chr15:40618200-40620600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:40618200-40625800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:40618200-40626000	Weak transcription	Stomach Mucosa	stomach
37	chr15:40618400-40619800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:40618400-40620400	Weak transcription	HepG2	liver
39	chr15:40618400-40620600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:40618400-40620600	Weak transcription	Adipose Nuclei	Adipose
41	chr15:40618400-40620600	Enhancers	Brain Anterior Caudate	brain
42	chr15:40618400-40621200	Enhancers	Right Ventricle	heart
43	chr15:40618400-40622200	Weak transcription	Brain Substantia Nigra	brain
44	chr15:40618400-40622400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:40618400-40622600	Genic enhancers	Osteobl	bone
46	chr15:40618400-40623000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:40618400-40624200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:40618400-40624400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:40618400-40624600	Weak transcription	Primary B cells from cord blood	blood
50	chr15:40618400-40625800	Weak transcription	Primary B cells from peripheral blood	blood

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