Variant report

Variant	rs2732480
Chromosome Location	chr12:48736303-48736304
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48735709..48737484-chr12:48748152..48750019,2	MCF-7	breast:
2	chr12:48731724..48737573-chr12:48737990..48746470,14	K562	blood:
3	chr12:48732421..48734160-chr12:48734497..48737400,2	MCF-7	breast:
4	chr12:48732035..48733570-chr12:48734227..48737131,2	MCF-7	breast:
5	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

Variant related genes	Relation type
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1107654	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2409003	0.83[ASN][1000 genomes]
rs2409004	0.83[ASN][1000 genomes]
rs2450994	0.95[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2468943	0.88[GIH][hapmap]
rs2468949	0.83[ASN][1000 genomes]
rs2634681	0.95[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2634682	0.83[ASN][1000 genomes]
rs2634684	0.95[GIH][hapmap];0.85[MEX][hapmap]
rs2634686	0.83[ASN][1000 genomes]
rs2634688	0.83[ASN][1000 genomes]
rs2634689	0.83[ASN][1000 genomes]
rs2732441	0.83[ASN][1000 genomes]
rs2732448	0.95[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2732453	0.83[ASN][1000 genomes]
rs2732454	0.83[ASN][1000 genomes]
rs2732457	0.95[GIH][hapmap];0.85[MEX][hapmap]
rs2732466	0.95[GIH][hapmap];0.85[MEX][hapmap]
rs2732481	0.95[GIH][hapmap]
rs2732484	0.95[GIH][hapmap];0.85[MEX][hapmap]
rs7315820	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs7486941	0.83[GIH][hapmap]
rs7487682	0.83[GIH][hapmap]
rs923397	0.95[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1044444	chr12:48725007-48737570	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
11	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2732480	ASB8	cis	cerebellum	SCAN
rs2732480	ZNF641	cis	multi-tissue	Pritchard
rs2732480	TMEM106C	cis	lymphoblastoid	seeQTL
rs2732480	ZNF641	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48723800-48736600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48725200-48736800	Weak transcription	Hela-S3	cervix
3	chr12:48728800-48736600	Weak transcription	Right Ventricle	heart
4	chr12:48728800-48737000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:48729000-48736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:48729000-48739200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:48729200-48736600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:48729200-48736600	Weak transcription	Fetal Intestine Small	intestine
9	chr12:48729200-48736600	Weak transcription	Pancreas	Pancrea
10	chr12:48729200-48743400	Weak transcription	Stomach Mucosa	stomach
11	chr12:48730200-48736600	Weak transcription	Ovary	ovary
12	chr12:48730400-48736400	Weak transcription	Lung	lung
13	chr12:48730600-48736800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:48731000-48736400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:48731200-48738200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:48731200-48743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:48731400-48736800	Weak transcription	Psoas Muscle	Psoas
18	chr12:48732000-48736600	Weak transcription	Gastric	stomach
19	chr12:48732000-48736600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:48732400-48736800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:48732400-48742600	Strong transcription	Left Ventricle	heart
22	chr12:48732600-48736600	Weak transcription	Osteobl	bone
23	chr12:48732600-48736800	Weak transcription	GM12878-XiMat	blood
24	chr12:48732600-48738000	Weak transcription	Small Intestine	intestine
25	chr12:48732600-48742600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:48732800-48736600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:48732800-48736600	Weak transcription	Esophagus	oesophagus
28	chr12:48732800-48737000	Weak transcription	NH-A	brain
29	chr12:48733200-48742000	Strong transcription	Brain Hippocampus Middle	brain
30	chr12:48733200-48742200	Strong transcription	Fetal Thymus	thymus
31	chr12:48733400-48736400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:48733400-48736400	Weak transcription	Aorta	Aorta
33	chr12:48733400-48739600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:48733400-48741000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:48733600-48736600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:48733600-48737400	Weak transcription	HepG2	liver
37	chr12:48733600-48742000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:48733600-48742200	Strong transcription	Primary B cells from cord blood	blood
39	chr12:48733600-48743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:48733800-48742000	Strong transcription	Liver	Liver
41	chr12:48733800-48742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:48733800-48742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:48734000-48736800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:48734000-48736800	Weak transcription	NHEK	skin
45	chr12:48734000-48741800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:48734000-48741800	Strong transcription	Fetal Brain Female	brain
47	chr12:48734000-48742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:48734000-48742200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:48734000-48742600	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:48734200-48736400	Weak transcription	HMEC	breast

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