Variant report

Variant	rs3846460
Chromosome Location	chr5:59817396-59817397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC109486.1-1	chr5:59816847-59822245	NONHSAT101638
2	lnc-AC109486.1-1	chr5:59816847-59822245	ENSG00000152931.7

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878197	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16878201	0.90[AMR][1000 genomes]
rs16878203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4133469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60446062	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568722	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093135	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093138	0.90[AMR][1000 genomes]
rs73093141	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110513	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73110526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7719584	0.83[AMR][1000 genomes]
rs7723069	1.00[AMR][1000 genomes]
rs7737012	0.96[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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59812800-59822400	Weak transcription	Brain Angular Gyrus	brain
2	chr5:59813800-59817600	Enhancers	Rectal Smooth Muscle	rectum
3	chr5:59814000-59819600	Enhancers	Colon Smooth Muscle	Colon
4	chr5:59814200-59817600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:59814800-59818800	Enhancers	Adipose Nuclei	Adipose
6	chr5:59815200-59818600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:59815800-59818400	Enhancers	Brain Hippocampus Middle	brain
8	chr5:59815800-59820600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr5:59816000-59818000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:59816000-59818400	Enhancers	HepG2	liver
11	chr5:59816000-59818800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr5:59816200-59817600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr5:59816200-59817600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:59816200-59817800	Enhancers	Aorta	Aorta
15	chr5:59816400-59818200	Weak transcription	Fetal Stomach	stomach
16	chr5:59816600-59817800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:59816600-59818400	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr5:59816600-59818600	Weak transcription	Placenta	Placenta
19	chr5:59816600-59819600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:59816800-59817800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:59816800-59817800	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr5:59816800-59818800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr5:59817000-59817400	Enhancers	Brain Substantia Nigra	brain
24	chr5:59817000-59817800	Weak transcription	Right Atrium	heart
25	chr5:59817000-59818000	Weak transcription	Left Ventricle	heart
26	chr5:59817000-59818200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:59817000-59818600	Enhancers	Primary T cells from cord blood	blood
28	chr5:59817000-59822000	Weak transcription	Fetal Thymus	thymus
29	chr5:59817200-59817400	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr5:59817200-59817600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:59817200-59817600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:59817200-59817600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:59817200-59817800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr5:59817200-59818000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr5:59817200-59818000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:59817200-59818000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:59817200-59818000	Enhancers	Dnd41	blood
38	chr5:59817200-59818400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr5:59817200-59818600	Active TSS	GM12878-XiMat	blood

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