Variant report

Variant	rs12109774
Chromosome Location	chr5:58388213-58388214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10065303	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065699	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10076635	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10452450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16889167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16889175	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs17720871	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17721133	0.95[CEU][hapmap]
rs17721311	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17721564	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17777280	0.96[CEU][hapmap]
rs17777617	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs56407743	0.93[EUR][1000 genomes]
rs62356683	0.82[EUR][1000 genomes]
rs62356684	0.82[EUR][1000 genomes]
rs62356686	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62356687	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62356690	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62356691	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62356692	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62356694	0.83[EUR][1000 genomes]
rs6898082	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs950446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58376400-58389200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:58376400-58390400	Weak transcription	Hela-S3	cervix
3	chr5:58378200-58391800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:58386200-58388400	Enhancers	Colon Smooth Muscle	Colon
5	chr5:58386400-58390200	Weak transcription	Fetal Brain Male	brain
6	chr5:58386400-58391000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58386600-58388400	Weak transcription	Fetal Kidney	kidney
8	chr5:58387200-58388400	Weak transcription	Fetal Heart	heart
9	chr5:58387200-58388600	Weak transcription	Small Intestine	intestine
10	chr5:58387600-58388400	Enhancers	Rectal Smooth Muscle	rectum
11	chr5:58387800-58394600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:58388000-58388400	Enhancers	HepG2	liver
13	chr5:58388000-58388400	Weak transcription	NHEK	skin
14	chr5:58388000-58388600	Enhancers	Primary T cells from cord blood	blood
15	chr5:58388000-58389200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr5:58388000-58389400	Active TSS	NHLF	lung
17	chr5:58388200-58388400	Enhancers	Duodenum Mucosa	Duodenum
18	chr5:58388200-58388600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:58388200-58389200	Flanking Active TSS	Fetal Lung	lung
20	chr5:58388200-58389200	Active TSS	A549	lung
21	chr5:58388200-58389400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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