Variant report

Variant	rs2546484
Chromosome Location	chr5:114844882-114844883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10038493	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10041776	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10043094	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs10053572	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10073505	0.81[ASN][1000 genomes]
rs10079000	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs1015812	0.87[ASN][1000 genomes]
rs12187973	0.85[CEU][hapmap]
rs13184723	0.87[ASN][1000 genomes]
rs13356084	0.94[ASN][1000 genomes]
rs13357862	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2032842	0.83[CHB][hapmap]
rs2546487	0.89[CEU][hapmap]
rs256938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256956	0.83[CEU][hapmap]
rs256959	0.82[CEU][hapmap]
rs256976	0.82[CEU][hapmap]
rs256977	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256989	0.86[ASN][1000 genomes]
rs256995	0.84[ASN][1000 genomes]
rs372702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860557	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878790	0.80[ASN][1000 genomes]
rs6892071	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6893854	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6894123	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs746566	0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs766454	0.87[ASN][1000 genomes]
rs813761	0.83[CEU][hapmap]
rs9326964	0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114843200-114854800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114843200-114858800	Weak transcription	Left Ventricle	heart
3	chr5:114843400-114845200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:114843600-114860000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:114843800-114845000	Weak transcription	Fetal Heart	heart
6	chr5:114844000-114847600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:114844000-114859000	Weak transcription	HSMMtube	muscle
8	chr5:114844200-114848000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:114844200-114849800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:114844200-114853200	Weak transcription	NHDF-Ad	bronchial
11	chr5:114844200-114854200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:114844200-114855000	Weak transcription	HSMM	muscle
13	chr5:114844200-114858000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:114844200-114858800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:114844200-114859800	Weak transcription	Osteobl	bone
16	chr5:114844800-114845400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:114844800-114846600	Enhancers	Cortex derived primary cultured neurospheres	brain

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