Variant report

Variant	rs7299225
Chromosome Location	chr12:105718631-105718632
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105716740..105719219-chr12:105722490..105724843,2	MCF-7	breast:
2	chr12:105712887..105714905-chr12:105718530..105720792,2	MCF-7	breast:
3	chr12:105715517..105717332-chr12:105717819..105719410,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10861371	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs11112434	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs11112465	0.82[MEX][hapmap]
rs11112467	1.00[ASN][1000 genomes]
rs11112475	1.00[CHB][hapmap]
rs1196742	1.00[ASN][1000 genomes]
rs1196745	1.00[ASN][1000 genomes]
rs1196748	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196749	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196754	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196756	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196765	1.00[ASN][1000 genomes]
rs1196777	1.00[CHB][hapmap]
rs1196780	0.85[GIH][hapmap]
rs1196793	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs1196795	1.00[GIH][hapmap]
rs1196797	1.00[GIH][hapmap]
rs1196805	1.00[ASN][1000 genomes]
rs1196806	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196807	1.00[ASN][1000 genomes]
rs1196808	1.00[ASN][1000 genomes]
rs1196813	1.00[CHB][hapmap]
rs1196817	1.00[CHB][hapmap]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CHB][hapmap]
rs1196852	1.00[CHB][hapmap]
rs1196853	1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	1.00[ASN][1000 genomes]
rs1196861	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196862	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196864	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196871	1.00[ASN][1000 genomes]
rs1196874	1.00[ASN][1000 genomes]
rs1206559	1.00[ASN][1000 genomes]
rs1209637	0.85[GIH][hapmap]
rs1211276	1.00[CHB][hapmap]
rs12822081	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2440715	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2440718	1.00[ASN][1000 genomes]
rs2464173	1.00[ASN][1000 genomes]
rs2888846	1.00[CHB][hapmap]
rs4545651	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7302174	1.00[CHB][hapmap]
rs7959385	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs935240	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs935241	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs935242	1.00[ASN][1000 genomes]
rs935244	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs9645791	1.00[CHB][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	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7299225	APPL2	cis	cerebellum	SCAN
rs7299225	KIAA1033	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105712400-105720000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:105712800-105719000	Weak transcription	NH-A	brain
3	chr12:105713400-105724000	Weak transcription	Pancreas	Pancrea
4	chr12:105713800-105720400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:105713800-105723800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:105714600-105720200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:105714600-105724000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:105715800-105719000	Enhancers	HSMM	muscle
9	chr12:105715800-105723800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:105716000-105723800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:105716200-105720400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:105716400-105720400	Weak transcription	A549	lung
13	chr12:105716400-105723800	Weak transcription	HSMMtube	muscle
14	chr12:105716600-105720600	Weak transcription	Osteobl	bone
15	chr12:105716600-105723600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:105716600-105723800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:105716800-105723600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:105716800-105723800	Weak transcription	Fetal Intestine Large	intestine
19	chr12:105717200-105720600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:105717800-105719000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:105717800-105719000	Enhancers	NHLF	lung
22	chr12:105717800-105719200	Enhancers	HMEC	breast
23	chr12:105718000-105719000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:105718000-105719000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr12:105718000-105719000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:105718000-105719800	Weak transcription	GM12878-XiMat	blood
27	chr12:105718000-105719800	Weak transcription	HUVEC	blood vessel
28	chr12:105718000-105720400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:105718000-105723800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:105718200-105720000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:105718200-105720200	Enhancers	NHDF-Ad	bronchial
32	chr12:105718200-105720400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:105718200-105721000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:105718200-105723800	Weak transcription	Stomach Mucosa	stomach
35	chr12:105718600-105718800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:105718600-105719000	Enhancers	Fetal Intestine Small	intestine
37	chr12:105718600-105719000	ZNF genes & repeats	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links