Variant report

Variant	rs10056328
Chromosome Location	chr5:152024369-152024370
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10037655	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10041396	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10041415	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10054152	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515675	0.81[AMR][1000 genomes]
rs10515676	0.81[AMR][1000 genomes]
rs11167585	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948856	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11956179	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11956651	0.81[AMR][1000 genomes]
rs12515178	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518097	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522538	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17113485	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17453880	0.92[EUR][1000 genomes]
rs34184277	0.93[ASN][1000 genomes]
rs35502931	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35558681	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4391148	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398624	0.83[AMR][1000 genomes]
rs4406125	0.81[AMR][1000 genomes]
rs4473762	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4484412	0.83[AMR][1000 genomes]
rs4487479	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4610448	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4612055	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4618416	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4958321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4958322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4958324	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958566	0.81[AMR][1000 genomes]
rs4958567	0.81[AMR][1000 genomes]
rs4958568	0.81[AMR][1000 genomes]
rs4958569	0.81[AMR][1000 genomes]
rs4958570	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4958571	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4958572	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57358310	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59126622	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60862272	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67979431	0.81[AMR][1000 genomes]
rs6863717	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869035	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6869129	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869968	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6871699	0.81[AMR][1000 genomes]
rs6871986	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6884556	0.81[AMR][1000 genomes]
rs6885111	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885419	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886482	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895232	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6895969	0.81[AMR][1000 genomes]
rs7730088	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9324734	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv5074	chr5:152010691-152055779	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10056328	SLC26A2	cis	cerebellum	SCAN
rs10056328	IL17B	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152022000-152024400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
2	chr5:152022200-152024400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr5:152022200-152029400	Weak transcription	Aorta	Aorta
4	chr5:152022400-152024600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:152022600-152024400	Enhancers	Fetal Kidney	kidney
6	chr5:152023800-152024400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:152023800-152024600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:152023800-152024600	Enhancers	Fetal Brain Female	brain
9	chr5:152024000-152024400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:152024000-152024600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:152024000-152024600	Enhancers	Brain Angular Gyrus	brain
12	chr5:152024000-152024600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr5:152024200-152024400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr5:152024200-152024600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:152024200-152024600	Enhancers	Esophagus	oesophagus

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