Variant report

Variant	rs12523625
Chromosome Location	chr5:127294777-127294778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:127294744..127297859-chr5:127418074..127420896,5	MCF-7	breast:
2	chr5:127292969..127298749-chr5:127417448..127421101,7	MCF-7	breast:
3	chr5:127263364..127266213-chr5:127293562..127295793,3	MCF-7	breast:
4	chr5:127293751..127296384-chr5:127304334..127306609,2	MCF-7	breast:
5	chr5:127211016..127213453-chr5:127292897..127295874,2	MCF-7	breast:
6	chr5:127293327..127295485-chr5:127298267..127301058,2	MCF-7	breast:
7	chr5:127293170..127295868-chr5:127299899..127303794,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10040931	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10041355	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10041388	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10052149	0.86[EUR][1000 genomes]
rs10055964	0.92[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10057048	0.86[EUR][1000 genomes]
rs10059403	0.89[CEU][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10074995	0.84[JPT][hapmap]
rs10076010	0.85[EUR][1000 genomes]
rs10079317	0.84[JPT][hapmap]
rs1013374	0.91[EUR][1000 genomes]
rs1013375	0.91[EUR][1000 genomes]
rs10463835	0.81[EUR][1000 genomes]
rs10463836	0.80[EUR][1000 genomes]
rs10478786	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478788	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10478790	0.85[EUR][1000 genomes]
rs10478791	0.80[EUR][1000 genomes]
rs10478792	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10519968	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10519977	0.85[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs10900794	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11740438	0.82[JPT][hapmap]
rs11740439	0.84[JPT][hapmap]
rs11745009	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11745023	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12517005	0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap]
rs12658023	0.84[JPT][hapmap]
rs13154863	0.82[EUR][1000 genomes]
rs13161109	0.83[EUR][1000 genomes]
rs13174053	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13177354	0.92[CEU][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs13180050	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13184942	0.80[EUR][1000 genomes]
rs13361741	0.84[JPT][hapmap]
rs1520246	0.84[JPT][hapmap]
rs1558149	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17606751	0.89[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2041143	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2108652	0.86[EUR][1000 genomes]
rs2108654	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159110	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2409037	0.81[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs2409038	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409039	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409040	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2898077	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34498802	0.82[EUR][1000 genomes]
rs35713319	0.85[EUR][1000 genomes]
rs4835934	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4836345	0.84[JPT][hapmap]
rs4836352	0.81[EUR][1000 genomes]
rs5008451	0.88[CEU][hapmap]
rs59634534	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6867103	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6867442	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6867465	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6867644	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6881456	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6889393	0.85[EUR][1000 genomes]
rs6892704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6897353	0.81[EUR][1000 genomes]
rs732235	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs732236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs768528	0.93[EUR][1000 genomes]
rs7711776	0.85[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs7713606	0.91[EUR][1000 genomes]
rs7717705	0.92[EUR][1000 genomes]
rs7722601	0.93[ASN][1000 genomes]
rs7732912	0.83[EUR][1000 genomes]
rs9327457	0.84[JPT][hapmap]
rs9327458	0.95[JPT][hapmap]
rs9327460	0.92[CEU][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9327461	0.85[EUR][1000 genomes]
rs9327462	0.85[CEU][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12523625	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
4	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
5	chr5:127281800-127295400	Weak transcription	Psoas Muscle	Psoas
6	chr5:127285200-127295200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:127286600-127295200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:127287400-127297200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:127288200-127295200	Weak transcription	Primary T cells from cord blood	blood
11	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
12	chr5:127290800-127295400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:127290800-127297400	Weak transcription	Spleen	Spleen
14	chr5:127291600-127295000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:127292200-127297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:127292400-127296400	Enhancers	Left Ventricle	heart
17	chr5:127292600-127296400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:127292600-127296400	Enhancers	HepG2	liver
19	chr5:127292600-127298400	Enhancers	Fetal Intestine Large	intestine
20	chr5:127292600-127298600	Enhancers	Fetal Intestine Small	intestine
21	chr5:127292800-127294800	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:127292800-127295000	Enhancers	Colon Smooth Muscle	Colon
23	chr5:127292800-127295200	Enhancers	Fetal Brain Female	brain
24	chr5:127292800-127295600	Enhancers	Brain Anterior Caudate	brain
25	chr5:127292800-127296200	Enhancers	Brain Substantia Nigra	brain
26	chr5:127292800-127296400	Enhancers	Brain Hippocampus Middle	brain
27	chr5:127292800-127297200	Enhancers	Fetal Lung	lung
28	chr5:127292800-127297600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr5:127292800-127297800	Enhancers	HUVEC	blood vessel
30	chr5:127292800-127298400	Enhancers	Fetal Heart	heart
31	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
32	chr5:127293000-127295200	Weak transcription	Osteobl	bone
33	chr5:127293000-127295600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:127293000-127295800	Flanking Active TSS	A549	lung
35	chr5:127293000-127297600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr5:127293000-127298600	Enhancers	Stomach Mucosa	stomach
37	chr5:127293200-127295000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:127293200-127295000	Weak transcription	NHLF	lung
39	chr5:127293200-127295400	Weak transcription	HSMM	muscle
40	chr5:127293200-127297400	Weak transcription	Gastric	stomach
41	chr5:127293200-127301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:127293200-127301800	Weak transcription	Ovary	ovary
43	chr5:127293200-127303600	Weak transcription	Esophagus	oesophagus
44	chr5:127293400-127294800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:127293400-127295000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:127293400-127295400	Weak transcription	NHDF-Ad	bronchial
47	chr5:127293400-127296200	Weak transcription	Right Ventricle	heart
48	chr5:127293400-127297200	Weak transcription	Right Atrium	heart
49	chr5:127293600-127294800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:127293600-127294800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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