Variant report

Variant	rs1525452
Chromosome Location	chr12:47542807-47542808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47540570..47543353-chr12:47547169..47548960,2	K562	blood:
2	chr12:47541282..47542895-chr12:47543869..47545971,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10785659	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10881048	0.87[CHB][hapmap]
rs10881049	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10881050	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881051	0.88[CEU][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs10881052	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs10881053	0.90[EUR][1000 genomes]
rs11183756	0.91[EUR][1000 genomes]
rs11612285	0.90[EUR][1000 genomes]
rs12578367	0.88[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs12579796	0.88[CEU][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12581006	0.91[CHB][hapmap]
rs12810420	0.92[EUR][1000 genomes]
rs12830116	0.87[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs1404812	0.88[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs1404813	0.84[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs1404814	0.89[EUR][1000 genomes]
rs1404819	0.87[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs1404820	0.83[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1404821	0.91[EUR][1000 genomes]
rs1581560	0.91[EUR][1000 genomes]
rs1917662	0.91[EUR][1000 genomes]
rs1917663	0.88[EUR][1000 genomes]
rs2091294	0.88[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2091295	0.91[EUR][1000 genomes]
rs2222609	0.92[EUR][1000 genomes]
rs2408714	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs2408715	0.92[EUR][1000 genomes]
rs2408716	0.91[CHB][hapmap]
rs4529959	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4533118	0.90[EUR][1000 genomes]
rs4544084	0.89[EUR][1000 genomes]
rs4598738	0.91[EUR][1000 genomes]
rs4768139	0.91[CHB][hapmap]
rs4768775	0.88[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs4768776	1.00[CHB][hapmap]
rs7484989	0.91[EUR][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1525452	C12orf68	cis	cerebellum	SCAN
rs1525452	SLC48A1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47508400-47545200	Weak transcription	HSMMtube	muscle
2	chr12:47527000-47547800	Weak transcription	Ovary	ovary
3	chr12:47535800-47549600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:47535800-47554600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:47536000-47549600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:47536000-47550000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:47536000-47550200	Weak transcription	Adipose Nuclei	Adipose
8	chr12:47536000-47550200	Weak transcription	Aorta	Aorta
9	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:47536200-47564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:47536400-47549400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:47539400-47550000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:47540000-47544800	Weak transcription	Primary T cells from cord blood	blood
14	chr12:47540000-47545200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:47540000-47545200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:47540000-47549200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:47540000-47549200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:47541600-47558400	Weak transcription	NHEK	skin
19	chr12:47541800-47549200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:47542000-47545200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:47542200-47543000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:47542400-47543800	Weak transcription	Spleen	Spleen
23	chr12:47542600-47543000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:47542800-47543400	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links