Variant report

Variant	rs56341652
Chromosome Location	chr5:59636174-59636175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10461451	0.88[AFR][1000 genomes]
rs12653863	0.88[AFR][1000 genomes]
rs13165296	0.92[EUR][1000 genomes]
rs13168619	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13171028	0.88[AFR][1000 genomes]
rs13172481	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34038162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34353877	0.88[AFR][1000 genomes]
rs35335033	0.89[EUR][1000 genomes]
rs35644384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35811820	0.88[AFR][1000 genomes]
rs35914313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36050835	0.88[AFR][1000 genomes]
rs4349679	0.88[AFR][1000 genomes]
rs4394088	0.88[AFR][1000 genomes]
rs4502776	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4699954	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57237852	0.91[AFR][1000 genomes]
rs6449466	0.87[AFR][1000 genomes]
rs6449468	0.88[AFR][1000 genomes]
rs6860626	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6862735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869495	0.89[EUR][1000 genomes]
rs71630006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7706560	0.92[EUR][1000 genomes]
rs7733705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59625200-59646800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59632600-59637200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:59635200-59636400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:59635200-59637400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:59635200-59638600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:59635400-59636200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:59635400-59636200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:59635400-59636200	Enhancers	NHDF-Ad	bronchial
9	chr5:59635400-59637200	Enhancers	Brain Cingulate Gyrus	brain
10	chr5:59635400-59637400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:59635600-59636200	Flanking Active TSS	Osteobl	bone
12	chr5:59635800-59637600	Enhancers	GM12878-XiMat	blood
13	chr5:59635800-59639200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:59636000-59636200	Active TSS	Stomach Smooth Muscle	stomach
15	chr5:59636000-59636400	Enhancers	Brain Angular Gyrus	brain
16	chr5:59636000-59637000	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:59636000-59637200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:59636000-59637200	Weak transcription	Aorta	Aorta
19	chr5:59636000-59637200	Enhancers	Brain Substantia Nigra	brain
20	chr5:59636000-59637400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:59636000-59637400	Enhancers	Brain Hippocampus Middle	brain
22	chr5:59636000-59637400	Enhancers	Fetal Brain Female	brain
23	chr5:59636000-59637800	Enhancers	Fetal Brain Male	brain

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