Variant report

Variant	rs662339
Chromosome Location	chr5:89316330-89316331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10044667	0.86[EUR][1000 genomes]
rs10805864	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942581	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11949266	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958908	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958926	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12517492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519494	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362216	0.85[ASN][1000 genomes]
rs154193	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560208	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs157305	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157306	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs157307	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157308	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157311	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157559	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157560	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157564	0.89[EUR][1000 genomes]
rs1596431	0.84[EUR][1000 genomes]
rs1645412	0.82[EUR][1000 genomes]
rs166820	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1698138	0.85[EUR][1000 genomes]
rs17589076	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs175965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2652732	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs280671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30713	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60448814	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6862722	0.86[EUR][1000 genomes]
rs6871792	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883728	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs818944	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs818945	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs818946	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs818947	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818948	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs889293	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924627	0.85[EUR][1000 genomes]
rs924628	0.85[EUR][1000 genomes]
rs9293534	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv882361	chr5:89302715-89357159	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89311800-89316400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:89311800-89316400	Weak transcription	HUVEC	blood vessel
3	chr5:89312000-89316400	Weak transcription	NH-A	brain
4	chr5:89312000-89316400	Weak transcription	Osteobl	bone
5	chr5:89312000-89317000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:89312200-89316400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:89312200-89317000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:89313000-89317000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:89313200-89316800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:89313200-89316800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:89313200-89317200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:89313400-89317000	Weak transcription	Aorta	Aorta
13	chr5:89313400-89317800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:89313800-89318000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:89313800-89318000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:89315800-89316400	Enhancers	GM12878-XiMat	blood
17	chr5:89316200-89317600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:89316200-89317600	Enhancers	Monocytes-CD14+_RO01746	blood

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