Variant report

Variant	rs13171028
Chromosome Location	chr5:59629421-59629422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10461451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12653863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168480	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423246	0.89[JPT][hapmap]
rs34038162	0.86[AFR][1000 genomes]
rs34353877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762247	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35811820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35914313	0.88[AFR][1000 genomes]
rs36050835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4394088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4409049	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4580739	0.83[JPT][hapmap]
rs4699954	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs56341652	0.88[AFR][1000 genomes]
rs57237852	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449466	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67522885	0.89[EUR][1000 genomes]
rs6860626	0.81[AFR][1000 genomes]
rs6861084	0.88[AFR][1000 genomes]
rs6862735	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs6897671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs71630006	0.88[AFR][1000 genomes]
rs7714394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7733705	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7735149	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737905	0.83[JPT][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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59620400-59631000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:59625200-59646800	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59626200-59630000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr5:59626600-59635800	Weak transcription	Fetal Stomach	stomach
5	chr5:59627200-59630400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:59627400-59630000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:59627800-59630200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:59628000-59631000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:59628000-59631000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:59628000-59631000	Enhancers	HMEC	breast
11	chr5:59628000-59631000	Enhancers	NHDF-Ad	bronchial
12	chr5:59628200-59630600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:59628200-59630600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:59628200-59630600	Enhancers	NHEK	skin
15	chr5:59628200-59631800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:59628600-59630200	Enhancers	NHLF	lung
17	chr5:59628600-59630400	Enhancers	Fetal Brain Male	brain
18	chr5:59628600-59630800	Enhancers	Hela-S3	cervix
19	chr5:59628600-59630800	Enhancers	Osteobl	bone
20	chr5:59628600-59631000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:59628600-59631000	Enhancers	NH-A	brain
22	chr5:59628800-59629800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:59628800-59630200	Enhancers	HSMM	muscle
24	chr5:59628800-59630600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:59628800-59631000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:59629000-59630000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:59629200-59630200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr5:59629200-59630400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:59629400-59631200	Enhancers	Aorta	Aorta

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