Variant report

Variant	rs12824565
Chromosome Location	chr12:46834693-46834694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46781028..46783722-chr12:46834423..46837382,2	K562	blood:
2	chr12:46834177..46835701-chr12:46837215..46839178,2	K562	blood:
3	chr12:46832578..46835564-chr12:46837748..46840595,2	K562	blood:
4	chr12:46762033..46769988-chr12:46831671..46842896,19	MCF-7	breast:
5	chr12:46760616..46768014-chr12:46824033..46835241,16	K562	blood:
6	chr12:46764438..46766456-chr12:46834331..46836982,2	K562	blood:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10748448	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10748450	0.86[EUR][1000 genomes]
rs10785627	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785628	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10785629	0.86[EUR][1000 genomes]
rs10880947	0.84[MEX][hapmap]
rs10880966	0.83[AMR][1000 genomes]
rs10880967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880968	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10880969	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880970	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880971	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs10880974	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11183478	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183479	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183483	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183484	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183488	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183504	0.89[MEX][hapmap]
rs1125909	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11561535	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12099669	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12298616	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12313929	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12314541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12319162	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12321960	0.83[YRI][hapmap]
rs12813763	0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs12814298	0.88[AMR][1000 genomes]
rs12814341	0.86[AMR][1000 genomes]
rs12822345	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832425	0.86[AMR][1000 genomes]
rs12832777	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1472178	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1472179	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1492895	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2131371	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2220727	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408497	0.81[AMR][1000 genomes]
rs2408498	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3936214	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4072304	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4076247	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs4077708	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4427617	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768119	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768121	0.90[AMR][1000 genomes]
rs4768122	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768123	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs4768709	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768710	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768711	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768712	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768713	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768714	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768715	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4768716	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768717	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768718	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768719	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768723	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768724	0.86[EUR][1000 genomes]
rs4768725	0.86[EUR][1000 genomes]
rs4768727	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs4768730	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs6582641	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6582642	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6582643	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6582646	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582657	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6582661	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6582663	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7134289	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301001	0.90[AMR][1000 genomes]
rs7311504	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312259	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7316127	0.84[MEX][hapmap]
rs7485580	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7485599	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7486495	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486532	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7486580	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486915	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7487828	0.83[AMR][1000 genomes]
rs7487877	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7488144	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7488450	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7489242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7954645	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7956314	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7959731	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7960808	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7964767	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7968897	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7976280	0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs7980455	0.80[CEU][hapmap]
rs7980775	0.85[MEX][hapmap]
rs9669404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9706460	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9706520	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9971879	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12824565	LALBA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:46825400-46844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:46825600-46843800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:46826400-46836000	Weak transcription	NH-A	brain
5	chr12:46826400-46839200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:46826600-46836400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:46826800-46836000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:46828000-46835800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:46830600-46834800	Enhancers	HUVEC	blood vessel
11	chr12:46831200-46838200	Weak transcription	K562	blood
12	chr12:46831200-46843200	Weak transcription	Left Ventricle	heart
13	chr12:46831600-46836000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:46832600-46836000	Enhancers	NHEK	skin
15	chr12:46832600-46836200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:46832800-46837200	Weak transcription	Pancreas	Pancrea
17	chr12:46832800-46837400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:46833600-46840800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:46834000-46834800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:46834000-46836000	Enhancers	Hela-S3	cervix
21	chr12:46834000-46844000	Weak transcription	Esophagus	oesophagus
22	chr12:46834400-46835200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:46834400-46835400	Weak transcription	HMEC	breast
24	chr12:46834400-46835800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:46834400-46835800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:46834400-46835800	Weak transcription	HSMM	muscle
27	chr12:46834400-46836000	Weak transcription	A549	lung
28	chr12:46834400-46836000	Weak transcription	NHDF-Ad	bronchial
29	chr12:46834400-46836000	Weak transcription	Osteobl	bone
30	chr12:46834400-46836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:46834400-46836200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:46834400-46836200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:46834400-46837200	Weak transcription	Psoas Muscle	Psoas
34	chr12:46834400-46846200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:46834600-46835600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:46834600-46835600	Weak transcription	NHLF	lung
37	chr12:46834600-46835800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links