Variant report

Variant	rs6882172
Chromosome Location	chr5:90576958-90576959
allele	A/G
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:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
2	chr5:90574103..90582351-chr5:90673173..90681609,28	K562	blood:
3	chr5:90574805..90578594-chr5:90673900..90681432,13	MCF-7	breast:
4	chr5:90575227..90576970-chr5:90607873..90610168,2	K562	blood:
5	chr15:83418877..83419415-chr5:90576252..90577188,2	Hela-S3	cervix:
6	chr5:90576418..90578111-chr5:90608143..90610210,2	K562	blood:
7	chr5:90573090..90582351-chr5:90673821..90680716,23	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-2	chr5:90575914-90576959	ENSG00000234292
2	lnc-GPR98-6	chr5:90575897-90578519	NONHSAT102741

No data

Variant related genes	Relation type
ENSG00000248323	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10038090	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10061355	0.88[ASN][1000 genomes]
rs10462343	0.97[ASN][1000 genomes]
rs10462492	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10474346	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10474347	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs12697807	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13171635	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1511344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1511345	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543066	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs1858309	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs2048451	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs2048452	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973441	0.86[ASN][1000 genomes]
rs4019243	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4019302	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364415	0.94[ASN][1000 genomes]
rs4377733	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4424024	0.89[ASN][1000 genomes]
rs4518439	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6859170	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869552	0.90[ASN][1000 genomes]
rs6885341	0.94[ASN][1000 genomes]
rs6888389	0.92[ASN][1000 genomes]
rs6888674	0.92[ASN][1000 genomes]
rs6889197	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6897578	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6898622	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7709572	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs7719516	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7724489	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90575000-90577000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:90575000-90577000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:90575200-90577000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr5:90575200-90577000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:90575200-90577000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr5:90575200-90577000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:90575200-90577000	Active TSS	Fetal Lung	lung
8	chr5:90575200-90577200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr5:90575200-90577200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:90575200-90577200	Active TSS	Fetal Brain Female	brain
11	chr5:90575200-90577400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:90575200-90577400	Flanking Active TSS	GM12878-XiMat	blood
13	chr5:90575200-90577600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:90575400-90577000	Active TSS	Brain Hippocampus Middle	brain
15	chr5:90575400-90577000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:90575400-90577000	Active TSS	Psoas Muscle	Psoas
17	chr5:90575400-90577000	Active TSS	Stomach Smooth Muscle	stomach
18	chr5:90575800-90577000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr5:90575800-90577200	Flanking Active TSS	K562	blood
20	chr5:90576000-90577000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:90576000-90577800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr5:90576200-90577000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:90576400-90577000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:90576400-90577000	Active TSS	Fetal Muscle Trunk	muscle
25	chr5:90576400-90577200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
26	chr5:90576400-90577400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:90576600-90577000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:90576600-90577000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:90576600-90577000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr5:90576600-90577000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr5:90576600-90577000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
32	chr5:90576600-90577000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr5:90576600-90577000	Flanking Active TSS	Fetal Heart	heart
34	chr5:90576600-90577000	Flanking Active TSS	Fetal Stomach	stomach
35	chr5:90576600-90577000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr5:90576600-90577000	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr5:90576600-90577000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr5:90576600-90577000	Flanking Active TSS	HMEC	breast
39	chr5:90576600-90577000	Flanking Active TSS	HSMM	muscle
40	chr5:90576600-90577000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr5:90576600-90577000	Flanking Active TSS	NHEK	skin
42	chr5:90576600-90577200	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr5:90576600-90577400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr5:90576600-90577400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr5:90576600-90577400	Flanking Active TSS	NH-A	brain
46	chr5:90576600-90577400	Flanking Active TSS	NHLF	lung
47	chr5:90576600-90577400	Flanking Active TSS	Osteobl	bone
48	chr5:90576600-90577600	Enhancers	Small Intestine	intestine
49	chr5:90576800-90577000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:90576800-90577000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links