Variant report

Variant	rs12081
Chromosome Location	chr15:40618613-40618614
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
2	chr15:40618049..40622052-chr15:40729021..40731269,3	K562	blood:
3	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:
4	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
5	chr15:40599147..40601689-chr15:40614013..40619011,4	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHGR1-1	chr15:40618596-40618916	ENSG00000259330.1
2	lnc-PHGR1-1	chr15:40616681-40618914	NONHSAT041825
3	lnc-PHGR1-1	chr15:40618596-40618913	NONHSAT041826
4	lnc-PHGR1-1	chr15:40617141-40618903	l_1150_chr15:40617140-40621361_brain

No data

Variant related genes	Relation type
ENSG00000252714	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000188549	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1077476	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]
rs11070264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2118961	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes]
rs2289333	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]
rs2289334	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4334271	0.95[JPT][hapmap]
rs4923863	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923864	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924455	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164564	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164747	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748245	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs882829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs934937	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40616400-40618800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:40617000-40619400	Enhancers	Spleen	Spleen
3	chr15:40617000-40622800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40617200-40619000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:40617200-40619600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:40617200-40630200	Weak transcription	A549	lung
7	chr15:40617400-40618800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr15:40617400-40619200	Weak transcription	Thymus	Thymus
9	chr15:40617400-40619800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:40617400-40621800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:40617400-40623000	Enhancers	Fetal Brain Male	brain
12	chr15:40617400-40623800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:40617400-40624000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:40617400-40626000	Weak transcription	Liver	Liver
15	chr15:40617400-40626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:40617400-40626400	Weak transcription	Pancreas	Pancrea
17	chr15:40617400-40627000	Weak transcription	Gastric	stomach
18	chr15:40617600-40618800	Enhancers	Colonic Mucosa	Colon
19	chr15:40617600-40619000	Enhancers	Placenta	Placenta
20	chr15:40617600-40619000	Enhancers	NH-A	brain
21	chr15:40617600-40619200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:40617600-40619400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr15:40617600-40620200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:40617600-40620200	Weak transcription	Fetal Kidney	kidney
25	chr15:40617600-40622400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:40617600-40623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:40617800-40619000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:40617800-40619000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:40617800-40619000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:40617800-40619800	Weak transcription	Ovary	ovary
31	chr15:40617800-40620000	Weak transcription	Primary T cells from cord blood	blood
32	chr15:40617800-40620000	Genic enhancers	HSMM	muscle
33	chr15:40617800-40620200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:40617800-40620600	Enhancers	Brain Cingulate Gyrus	brain
35	chr15:40617800-40623000	Enhancers	HMEC	breast
36	chr15:40617800-40625000	Weak transcription	Psoas Muscle	Psoas
37	chr15:40618000-40618800	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:40618000-40619000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:40618000-40619000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr15:40618000-40619000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:40618000-40619200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr15:40618000-40619200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr15:40618000-40619400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr15:40618000-40619600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:40618000-40620000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:40618000-40620400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:40618000-40622600	Weak transcription	NHLF	lung
48	chr15:40618000-40624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:40618000-40624400	Enhancers	NHDF-Ad	bronchial
50	chr15:40618000-40625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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