Variant report

Variant	rs1588730
Chromosome Location	chr4:89955623-89955624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10000140	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027874	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030342	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097210	0.87[CEU][hapmap]
rs11097211	0.87[CEU][hapmap]
rs11734085	1.00[ASN][1000 genomes]
rs12506327	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507819	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113298	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115669	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120109	1.00[ASN][1000 genomes]
rs13137443	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138946	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13140085	0.87[CEU][hapmap]
rs13150503	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513817	1.00[ASN][1000 genomes]
rs17014936	1.00[YRI][hapmap]
rs17014963	1.00[YRI][hapmap]
rs17770341	1.00[ASN][1000 genomes]
rs17821540	1.00[ASN][1000 genomes]
rs17823587	1.00[ASN][1000 genomes]
rs2056012	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195755	1.00[ASN][1000 genomes]
rs33998578	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34008667	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34075854	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34300408	1.00[ASN][1000 genomes]
rs34624010	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35130975	0.89[EUR][1000 genomes]
rs35652620	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909707	1.00[ASN][1000 genomes]
rs36111123	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004788	1.00[ASN][1000 genomes]
rs62304457	0.81[AMR][1000 genomes]
rs62306389	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308627	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814023	1.00[ASN][1000 genomes]
rs6823660	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826407	0.87[CEU][hapmap]
rs6856010	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668782	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992522	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:89940200-89957800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:89940400-89956600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:89940400-89956600	Weak transcription	NH-A	brain
6	chr4:89940400-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:89940400-89957800	Weak transcription	Aorta	Aorta
8	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:89940600-89956000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:89940600-89956000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:89940600-89957800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:89940600-89957800	Weak transcription	Ovary	ovary
14	chr4:89940800-89956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:89941200-89956000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:89941200-89956200	Weak transcription	Fetal Lung	lung
17	chr4:89941800-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:89941800-89957800	Weak transcription	Fetal Stomach	stomach
19	chr4:89944200-89958000	Weak transcription	Fetal Heart	heart
20	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
21	chr4:89945600-89957400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:89945600-89963000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:89946200-89972800	Weak transcription	A549	lung
24	chr4:89949000-89957000	Weak transcription	K562	blood
25	chr4:89949200-89956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:89949800-89956000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:89949800-89957400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:89950800-89956800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:89950800-89957200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:89954200-89957800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:89955600-89958200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links