Variant report

Variant	rs12061689
Chromosome Location	chr1:186110557-186110558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186110390..186113261-chr1:186118377..186120080,2	MCF-7	breast:
2	chr1:186107103..186108701-chr1:186110492..186112868,2	MCF-7	breast:
3	chr1:186058150..186059707-chr1:186108819..186111468,2	K562	blood:
4	chr1:186109391..186111607-chr1:186111701..186113475,2	MCF-7	breast:
5	chr1:186110179..186113621-chr1:186114137..186116507,5	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489755	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489756	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10752962	0.93[ASN][1000 genomes]
rs10798035	0.86[CHD][hapmap]
rs10798037	0.88[ASN][1000 genomes]
rs10911810	0.86[CHD][hapmap]
rs10911812	0.82[CHD][hapmap]
rs10911813	0.82[CHD][hapmap]
rs10911825	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911826	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911828	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911829	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12078939	0.80[ASN][1000 genomes]
rs12080760	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs12122227	0.84[ASN][1000 genomes]
rs12124204	0.87[ASN][1000 genomes]
rs12133656	0.89[ASN][1000 genomes]
rs12565788	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs1322374	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs1358936	0.88[ASN][1000 genomes]
rs1407434	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2057387	0.84[ASN][1000 genomes]
rs2057388	0.84[ASN][1000 genomes]
rs2146098	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2224575	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2383431	0.81[CHD][hapmap]
rs2891230	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs3737941	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3845367	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4233125	0.84[CHD][hapmap]
rs4528072	0.83[ASN][1000 genomes]
rs4535962	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650694	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4650695	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4651298	0.82[CHD][hapmap]
rs4651300	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6425015	0.82[CHD][hapmap]
rs6425017	0.81[CHD][hapmap]
rs6659783	0.87[ASN][1000 genomes]
rs6664918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6673390	0.95[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.95[ASN][1000 genomes]
rs6689111	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6696910	0.87[ASN][1000 genomes]
rs6698064	0.84[ASN][1000 genomes]
rs6702313	0.84[ASN][1000 genomes]
rs6703518	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs721153	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7516516	0.98[ASN][1000 genomes]
rs7545010	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7549552	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs7550425	0.82[CHD][hapmap]
rs7552198	0.94[ASN][1000 genomes]
rs9286859	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9286860	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs970578	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12061689	CACNA1E	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186046400-186135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:186052200-186118200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:186064600-186113200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:186073000-186121400	Weak transcription	NH-A	brain
5	chr1:186075000-186113600	Weak transcription	Lung	lung
6	chr1:186080400-186121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:186100000-186113200	Weak transcription	Left Ventricle	heart
8	chr1:186100000-186113400	Weak transcription	Aorta	Aorta
9	chr1:186107200-186115000	Weak transcription	Adipose Nuclei	Adipose
10	chr1:186107400-186114600	Weak transcription	Liver	Liver
11	chr1:186107600-186113400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:186108000-186115800	Weak transcription	Fetal Lung	lung
13	chr1:186109000-186121400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:186109200-186124600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:186109400-186121200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:186109600-186113600	Weak transcription	Ovary	ovary
17	chr1:186109600-186115800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:186109600-186121200	Weak transcription	Osteobl	bone
19	chr1:186109800-186115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:186109800-186121400	Weak transcription	NHDF-Ad	bronchial
21	chr1:186109800-186121600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:186110000-186113400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:186110000-186121200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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