Variant report

Variant	rs503548
Chromosome Location	chr12:118812423-118812424
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:118812323-118814598	K562	blood:	n/a	chr12:118813524-118813534 chr12:118813526-118813535

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:118666340..118669274-chr12:118811225..118812911,2	MCF-7	breast:
2	chr12:118751783..118754702-chr12:118810776..118812505,2	K562	blood:
3	chr12:118670146..118671959-chr12:118810899..118813142,2	MCF-7	breast:
4	chr12:118577698..118580180-chr12:118811113..118813216,2	MCF-7	breast:
5	chr12:118674302..118676883-chr12:118810896..118813058,3	MCF-7	breast:
6	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
7	chr12:118558717..118560861-chr12:118811542..118813614,2	K562	blood:
8	chr12:118601731..118605413-chr12:118811549..118815749,6	MCF-7	breast:
9	chr12:118573102..118576254-chr12:118808901..118815960,7	MCF-7	breast:
10	chr12:118604051..118606436-chr12:118810994..118813151,2	MCF-7	breast:
11	chr12:118791019..118798938-chr12:118809011..118813946,9	MCF-7	breast:
12	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:
13	chr12:118612128..118614340-chr12:118811467..118813100,2	MCF-7	breast:
14	chr12:118638724..118640594-chr12:118810784..118812979,2	K562	blood:

No data

Variant related genes	Relation type
TAOK3	TF binding region
SUDS3	TF binding region
ENSG00000089220	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000221280	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1092854	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1151901	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1277175	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs2062522	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs353887	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs353896	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap]
rs364823	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap]
rs404566	0.81[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs410747	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs418941	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs484838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494005	0.83[ASN][1000 genomes]
rs519480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523011	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571113	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575121	0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7136004	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7307953	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7795	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs793596	0.96[ASN][1000 genomes]
rs795481	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs503548	PEBP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118811200-118812600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr12:118811200-118813800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:118811200-118813800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:118811200-118813800	Weak transcription	Gastric	stomach
5	chr12:118811200-118813800	Weak transcription	Pancreas	Pancrea
6	chr12:118811400-118812600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:118811400-118812800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:118811400-118813600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:118811400-118813800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:118811400-118813800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:118811400-118813800	Weak transcription	Aorta	Aorta
12	chr12:118811400-118813800	Weak transcription	Esophagus	oesophagus
13	chr12:118811400-118813800	Weak transcription	Lung	lung
14	chr12:118811600-118813200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:118811600-118813200	Enhancers	Brain Angular Gyrus	brain
16	chr12:118811600-118813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:118811600-118813600	Weak transcription	Placenta	Placenta
18	chr12:118811600-118813800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:118811600-118813800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:118811600-118813800	Weak transcription	Ovary	ovary
21	chr12:118811800-118812600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:118811800-118812600	Enhancers	Fetal Muscle Leg	muscle
23	chr12:118811800-118812600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:118811800-118812800	Enhancers	Adipose Nuclei	Adipose
25	chr12:118811800-118812800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:118811800-118812800	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:118811800-118812800	Weak transcription	Brain Substantia Nigra	brain
28	chr12:118811800-118812800	Enhancers	Osteobl	bone
29	chr12:118811800-118813000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:118811800-118813000	Enhancers	NHEK	skin
31	chr12:118811800-118813200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:118811800-118813200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:118811800-118813200	Weak transcription	Brain Anterior Caudate	brain
34	chr12:118811800-118813200	Enhancers	NHLF	lung
35	chr12:118811800-118813400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:118811800-118813400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:118811800-118813400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:118811800-118813400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:118811800-118813400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:118811800-118813400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:118811800-118813400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:118811800-118813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:118811800-118813400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:118811800-118813400	Weak transcription	Brain Germinal Matrix	brain
45	chr12:118811800-118813400	Enhancers	Fetal Heart	heart
46	chr12:118811800-118813400	Weak transcription	Fetal Lung	lung
47	chr12:118811800-118813400	Weak transcription	Fetal Stomach	stomach
48	chr12:118811800-118813400	Weak transcription	Fetal Thymus	thymus
49	chr12:118811800-118813400	Weak transcription	NH-A	brain
50	chr12:118811800-118813600	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links