Variant report

Variant	rs2249624
Chromosome Location	chr12:118589069-118589070
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:118481881..118483634-chr12:118588470..118590195,2	MCF-7	breast:
2	chr12:118587989..118589650-chr12:118590135..118591829,2	MCF-7	breast:
3	chr12:118587254..118590333-chr12:118591083..118593849,3	K562	blood:
4	chr12:118581884..118587240-chr12:118588010..118590251,5	K562	blood:
5	chr12:118587155..118589565-chr12:118812730..118814697,2	K562	blood:
6	chr12:118580920..118583677-chr12:118588171..118589685,2	K562	blood:
7	chr12:118587720..118589870-chr12:118590427..118592560,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1051175	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051470	0.82[CEU][hapmap]
rs1092854	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1151901	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap]
rs1277175	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1726386	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1726407	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2018619	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088702	0.88[ASW][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap]
rs2463173	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353885	0.81[ASN][1000 genomes]
rs353886	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs353887	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs353889	0.85[ASN][1000 genomes]
rs353896	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs364823	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs404566	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs418941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs461499	0.82[ASW][hapmap];0.86[JPT][hapmap]
rs575121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs795473	0.89[ASN][1000 genomes]
rs795481	0.96[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs795482	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980628	0.85[JPT][hapmap]
rs904661	0.82[CEU][hapmap]
rs904662	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2249624	PEBP1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118575400-118590400	Strong transcription	Fetal Muscle Trunk	muscle
2	chr12:118575400-118590600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:118575400-118590600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:118575400-118591400	Strong transcription	Fetal Stomach	stomach
5	chr12:118575600-118601600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:118575800-118589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:118575800-118590400	Strong transcription	Lung	lung
8	chr12:118575800-118590600	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:118575800-118590800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr12:118576000-118591600	Strong transcription	Fetal Intestine Large	intestine
11	chr12:118576000-118591600	Strong transcription	Dnd41	blood
12	chr12:118576000-118601200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
15	chr12:118576200-118590400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:118576200-118590600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:118576200-118591000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:118576200-118591400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:118576200-118595400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:118576400-118591400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:118576600-118590600	Strong transcription	Adipose Nuclei	Adipose
22	chr12:118576600-118590600	Strong transcription	Brain Germinal Matrix	brain
23	chr12:118577400-118601800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:118577600-118590800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:118577600-118599000	Weak transcription	Psoas Muscle	Psoas
26	chr12:118578000-118590800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:118578200-118611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:118578600-118603200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:118580400-118590600	Strong transcription	Spleen	Spleen
30	chr12:118581400-118590400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:118583800-118589800	Weak transcription	Right Ventricle	heart
32	chr12:118583800-118595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:118583800-118598000	Weak transcription	HUVEC	blood vessel
34	chr12:118584000-118589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:118584000-118590000	Weak transcription	Fetal Brain Male	brain
36	chr12:118584000-118591200	Strong transcription	Liver	Liver
37	chr12:118584000-118595000	Weak transcription	HSMMtube	muscle
38	chr12:118584000-118595200	Weak transcription	HSMM	muscle
39	chr12:118584000-118595600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:118584200-118595200	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:118584400-118591400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:118584800-118589600	Weak transcription	NHEK	skin
44	chr12:118584800-118591600	Strong transcription	Fetal Brain Female	brain
45	chr12:118585000-118589600	Strong transcription	A549	lung
46	chr12:118585200-118589200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:118585200-118589400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:118585600-118589200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:118585600-118589800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:118585600-118590000	Weak transcription	H9 Cell Line	embryonic stem cell

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