Variant report

Variant	rs3846459
Chromosome Location	chr5:59816304-59816305
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:25)

rs_ID	r²[population]
rs10516153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878197	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16878201	0.90[AMR][1000 genomes]
rs16878203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878228	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857233	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857234	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4133469	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60446062	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568722	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093135	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093138	0.90[AMR][1000 genomes]
rs73093141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110513	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73110526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7719584	0.83[AMR][1000 genomes]
rs7723069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7737012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59812800-59816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:59812800-59822400	Weak transcription	Brain Angular Gyrus	brain
3	chr5:59813800-59817600	Enhancers	Rectal Smooth Muscle	rectum
4	chr5:59814000-59819600	Enhancers	Colon Smooth Muscle	Colon
5	chr5:59814200-59817600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:59814400-59816600	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:59814400-59816600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:59814600-59816400	Enhancers	Fetal Stomach	stomach
9	chr5:59814800-59818800	Enhancers	Adipose Nuclei	Adipose
10	chr5:59815200-59816800	Enhancers	Stomach Smooth Muscle	stomach
11	chr5:59815200-59817200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:59815200-59818600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:59815400-59817000	Enhancers	Stomach Mucosa	stomach
14	chr5:59815800-59818400	Enhancers	Brain Hippocampus Middle	brain
15	chr5:59815800-59820600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr5:59816000-59816400	Enhancers	Pancreas	Pancrea
17	chr5:59816000-59816800	Enhancers	Fetal Muscle Leg	muscle
18	chr5:59816000-59816800	Enhancers	Gastric	stomach
19	chr5:59816000-59816800	Flanking Active TSS	GM12878-XiMat	blood
20	chr5:59816000-59817000	Enhancers	Left Ventricle	heart
21	chr5:59816000-59817000	Enhancers	Right Atrium	heart
22	chr5:59816000-59817000	Enhancers	Right Ventricle	heart
23	chr5:59816000-59818000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:59816000-59818400	Enhancers	HepG2	liver
25	chr5:59816000-59818800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr5:59816200-59816400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr5:59816200-59816600	Enhancers	Placenta	Placenta
28	chr5:59816200-59816800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:59816200-59817000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:59816200-59817000	Enhancers	Fetal Thymus	thymus
31	chr5:59816200-59817000	Enhancers	Spleen	Spleen
32	chr5:59816200-59817200	Enhancers	Primary hematopoietic stem cells	blood
33	chr5:59816200-59817600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:59816200-59817600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:59816200-59817800	Enhancers	Aorta	Aorta

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