Variant report

Variant	rs17633648
Chromosome Location	chr4:152158519-152158520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10020317	0.85[JPT][hapmap]
rs10434137	0.85[JPT][hapmap]
rs10520101	0.85[JPT][hapmap]
rs10520102	0.85[JPT][hapmap]
rs10776522	0.85[JPT][hapmap]
rs10857253	0.85[JPT][hapmap]
rs11733964	0.85[JPT][hapmap]
rs11734577	0.85[JPT][hapmap]
rs11934792	0.85[JPT][hapmap]
rs12503016	0.92[ASN][1000 genomes]
rs12504166	0.98[ASN][1000 genomes]
rs12505974	0.85[JPT][hapmap]
rs12508270	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12510153	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12511209	0.93[ASN][1000 genomes]
rs12512856	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs12644496	0.85[JPT][hapmap]
rs12647306	0.85[JPT][hapmap]
rs13101417	0.85[JPT][hapmap]
rs13141515	0.84[JPT][hapmap]
rs13145829	0.85[JPT][hapmap]
rs17633530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17633537	0.93[ASN][1000 genomes]
rs17633600	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.98[ASN][1000 genomes]
rs17633654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875308	1.00[CEU][hapmap]
rs2280280	0.83[JPT][hapmap]
rs2280283	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2407167	1.00[CEU][hapmap]
rs2407168	1.00[CEU][hapmap]
rs2407220	1.00[CEU][hapmap]
rs2407221	1.00[CEU][hapmap]
rs2407412	0.85[JPT][hapmap]
rs2407417	0.85[JPT][hapmap]
rs2897659	0.85[JPT][hapmap]
rs3736502	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3792611	0.85[JPT][hapmap]
rs4266274	0.85[JPT][hapmap]
rs4696234	0.85[JPT][hapmap]
rs4696658	0.85[JPT][hapmap]
rs58496896	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59944801	0.99[ASN][1000 genomes]
rs60212468	0.99[ASN][1000 genomes]
rs60367453	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60761330	1.00[ASN][1000 genomes]
rs61442068	0.81[ASN][1000 genomes]
rs6535764	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6535784	1.00[CEU][hapmap]
rs6846323	0.85[JPT][hapmap]
rs6850311	1.00[CEU][hapmap]
rs72967545	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7439970	0.83[JPT][hapmap]
rs7656771	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7664483	0.85[JPT][hapmap]
rs7669180	0.85[JPT][hapmap]
rs7671332	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681468	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7691584	0.85[JPT][hapmap]
rs7699574	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17633648	RPS3A	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
3	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:152141000-152167400	Weak transcription	HepG2	liver
5	chr4:152144800-152163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:152147200-152160200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152148000-152164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:152148200-152163400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:152149200-152159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:152149200-152172000	Weak transcription	Left Ventricle	heart
11	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:152149600-152159600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:152149600-152173000	Weak transcription	Right Atrium	heart
15	chr4:152150200-152158600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:152152400-152159800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:152154000-152159600	Weak transcription	Adipose Nuclei	Adipose
18	chr4:152154200-152159200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:152154200-152159600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:152155000-152159800	Weak transcription	Ovary	ovary
21	chr4:152155800-152159000	Weak transcription	Brain Anterior Caudate	brain
22	chr4:152155800-152159200	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:152155800-152159600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:152155800-152159600	Weak transcription	Brain Substantia Nigra	brain
25	chr4:152155800-152159600	Weak transcription	Fetal Lung	lung
26	chr4:152156000-152179800	Weak transcription	Fetal Stomach	stomach
27	chr4:152156200-152159600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:152156200-152163400	Weak transcription	Fetal Heart	heart
29	chr4:152157600-152167800	Weak transcription	Fetal Intestine Large	intestine
30	chr4:152158000-152158800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr4:152158200-152158800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:152158200-152158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:152158200-152160000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:152158400-152159600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:152158400-152161600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:152158400-152161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:152158400-152162800	Weak transcription	Fetal Intestine Small	intestine
38	chr4:152158400-152163200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:152158400-152163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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