Variant report

Variant	rs10022539
Chromosome Location	chr4:87847613-87847614
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87846751..87849645-chr4:87881394..87883091,2	K562	blood:
2	chr4:87846087..87848184-chr4:88034153..88037077,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87847594..87849419-chr4:87893253..87895027,2	MCF-7	breast:
5	chr4:87846783..87849156-chr4:87926665..87928343,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13102958	0.82[ASN][1000 genomes]
rs13116978	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1584346	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053775	0.81[ASN][1000 genomes]
rs2594277	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2594278	0.93[ASN][1000 genomes]
rs2594279	0.94[ASN][1000 genomes]
rs2705616	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705618	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2785	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109038	0.82[ASN][1000 genomes]
rs3113493	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113494	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113495	0.94[ASN][1000 genomes]
rs4274814	0.81[ASN][1000 genomes]
rs4536898	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825600-87849400	Weak transcription	Lung	lung
2	chr4:87825600-87849400	Weak transcription	Spleen	Spleen
3	chr4:87825800-87854800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:87825800-87854800	Weak transcription	Right Ventricle	heart
5	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
6	chr4:87826000-87852400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:87829800-87855000	Weak transcription	Aorta	Aorta
8	chr4:87830200-87849600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:87830400-87847800	Weak transcription	Psoas Muscle	Psoas
11	chr4:87830400-87849400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:87830400-87854600	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:87831000-87855000	Weak transcription	Fetal Lung	lung
14	chr4:87831400-87854400	Weak transcription	Fetal Heart	heart
15	chr4:87831400-87854800	Weak transcription	Right Atrium	heart
16	chr4:87832200-87854800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:87835200-87849000	Weak transcription	Pancreas	Pancrea
18	chr4:87837200-87854400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:87838400-87855000	Weak transcription	Colonic Mucosa	Colon
20	chr4:87839000-87850200	Enhancers	Placenta	Placenta
21	chr4:87840200-87852200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:87840200-87854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:87840400-87847800	Weak transcription	HSMMtube	muscle
24	chr4:87840400-87849000	Weak transcription	GM12878-XiMat	blood
25	chr4:87842600-87855400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:87843600-87848800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:87843600-87849200	Weak transcription	Adipose Nuclei	Adipose
28	chr4:87843800-87849200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:87843800-87854600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:87844000-87847800	Weak transcription	Stomach Mucosa	stomach
31	chr4:87844000-87848800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:87844000-87848800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:87844000-87848800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:87844000-87849200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:87844000-87849400	Weak transcription	Liver	Liver
36	chr4:87844000-87849400	Weak transcription	Esophagus	oesophagus
37	chr4:87844000-87854600	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:87844000-87854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:87844000-87854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:87844000-87854800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:87844000-87855000	Weak transcription	Brain Substantia Nigra	brain
42	chr4:87844000-87855000	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:87844200-87849200	Weak transcription	Ovary	ovary
44	chr4:87844400-87852200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:87845200-87849800	Enhancers	HUVEC	blood vessel
46	chr4:87845400-87849800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:87845400-87849800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:87845400-87850400	Enhancers	HMEC	breast
49	chr4:87845600-87847800	Enhancers	NHEK	skin
50	chr4:87845600-87849800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links