Variant report

Variant	rs4720624
Chromosome Location	chr7:47954163-47954164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1056663	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1879833	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1879834	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2242477	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2242478	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2242479	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs2686816	0.86[CHB][hapmap]
rs2686817	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2686820	0.82[ASN][1000 genomes]
rs2686821	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2686823	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2686825	0.80[ASN][1000 genomes]
rs2686830	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2686831	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2686832	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2686835	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2686836	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2686838	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2708861	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2708862	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2708873	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2708875	0.81[CHB][hapmap]
rs2708878	0.82[ASN][1000 genomes]
rs2708880	0.80[ASN][1000 genomes]
rs2708894	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2708895	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2708903	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2708905	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2708910	0.80[ASN][1000 genomes]
rs2708911	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs3176478	0.83[JPT][hapmap]
rs3176564	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs35051223	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35719200	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60107343	0.82[ASN][1000 genomes]
rs67565252	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885337	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs939904	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs939905	0.86[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs953572	0.81[CEU][hapmap]
rs9648569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4720624	UPP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47928400-47957600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
3	chr7:47945200-47954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:47945400-47954200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:47948600-47954600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:47949000-47954200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:47949000-47954400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:47949200-47956000	Weak transcription	Left Ventricle	heart
9	chr7:47949200-47956000	Weak transcription	Lung	lung
10	chr7:47953000-47954200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:47953400-47954800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:47954000-47955000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:47954000-47955200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:47954000-47955200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:47954000-47956200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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