Variant report

Variant	rs6877420
Chromosome Location	chr5:90606574-90606575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
2	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
3	chr5:90605455..90607688-chr5:90608223..90610008,2	K562	blood:
4	chr5:90595076..90597683-chr5:90606068..90607704,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-1	chr5:90603398-90606849	XLOC_004924
2	lnc-ARRDC3-1	chr5:90599690-90606849	XLOC_004924
3	lnc-ARRDC3-1	chr5:90606277-90606849	XLOC_004924
4	lnc-ARRDC3-1	chr5:90601497-90608312	NONHSAT102743

No data

Variant related genes	Relation type
ENSG00000234292	Chromatin interaction
ENSG00000248323	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10057046	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10462494	0.93[ASN][1000 genomes]
rs10462495	0.93[ASN][1000 genomes]
rs13356765	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2048453	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2137007	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916853	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916854	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4916857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865066	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865269	0.93[ASN][1000 genomes]
rs6880312	0.93[ASN][1000 genomes]
rs7704529	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7721772	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727557	0.93[ASN][1000 genomes]
rs7732832	0.96[ASN][1000 genomes]
rs9293562	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9293564	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90589800-90607400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:90593000-90607000	Weak transcription	Left Ventricle	heart
3	chr5:90593000-90607000	Weak transcription	HSMMtube	muscle
4	chr5:90598000-90606800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:90598000-90607000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:90599000-90607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:90600400-90607000	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:90600800-90607200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:90601800-90607000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:90602200-90607200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:90602200-90607200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:90602600-90608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:90603000-90606600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:90603000-90607000	Weak transcription	Right Atrium	heart
15	chr5:90603200-90606600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:90603200-90606600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:90603200-90607000	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:90603400-90606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:90603400-90606800	Weak transcription	NHEK	skin
20	chr5:90603600-90606600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:90603600-90606800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:90603800-90606600	Weak transcription	HMEC	breast
23	chr5:90603800-90606800	Weak transcription	NHLF	lung
24	chr5:90603800-90607000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:90603800-90607000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:90604000-90606800	Weak transcription	Osteobl	bone
27	chr5:90604000-90607000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:90604200-90606800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:90604200-90606800	Weak transcription	NHDF-Ad	bronchial
30	chr5:90604600-90606600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:90605200-90609000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr5:90605400-90606800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr5:90605400-90607200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:90605400-90611200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr5:90605600-90606800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:90605600-90607000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:90605600-90610200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:90605800-90607000	Enhancers	Dnd41	blood
39	chr5:90605800-90608400	Enhancers	Primary B cells from peripheral blood	blood
40	chr5:90605800-90610400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:90605800-90610400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr5:90605800-90611200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:90606000-90606800	Enhancers	Primary B cells from cord blood	blood
44	chr5:90606000-90607000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr5:90606000-90607000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:90606000-90607000	Weak transcription	Psoas Muscle	Psoas
47	chr5:90606000-90607000	Weak transcription	Thymus	Thymus
48	chr5:90606000-90607200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
49	chr5:90606000-90611200	Enhancers	Fetal Thymus	thymus
50	chr5:90606200-90606600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links