Variant report

Variant	rs4498770
Chromosome Location	chr1:184638266-184638267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184637359..184638932-chr1:184640228..184642032,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EDEM3-1	chr1:184638176-184638544	XLOC_001125

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1040666	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1046239	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1061508	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs10752941	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10797987	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911640	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12043236	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12071631	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12124929	0.83[GIH][hapmap]
rs12567225	0.83[GIH][hapmap]
rs12567226	0.83[GIH][hapmap]
rs2024765	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024767	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2207733	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2333715	0.83[GIH][hapmap]
rs2333716	0.92[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3736757	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3895196	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs4469687	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4651230	0.81[GIH][hapmap]
rs6663178	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6677073	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726427	0.88[CEU][hapmap]
rs7523023	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7525074	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs861575	0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs861578	0.87[GIH][hapmap]
rs861581	0.86[GIH][hapmap]
rs9425339	0.83[ASN][1000 genomes]
rs9425341	0.83[EUR][1000 genomes]
rs9425343	0.83[GIH][hapmap]
rs9425633	0.84[EUR][1000 genomes]
rs9658937	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9661314	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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 target site	69 gene(s)	inside rSNPs	diseases
5	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv947339	chr1:184618714-184641256	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4498770	ABL2	cis	cerebellum	SCAN
rs4498770	PRG4	cis	parietal	SCAN
rs4498770	EDEM3	cis	Artery Tibial	GTEx
rs4498770	EDEM3	cis	Esophagus Muscularis	GTEx
rs4498770	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs4498770	EDEM3	cis	Nerve Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184633600-184638400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:184634000-184638400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:184634800-184641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:184636200-184639000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:184636400-184639000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:184636400-184643200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:184637000-184639200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:184637200-184638400	Weak transcription	Fetal Lung	lung
9	chr1:184637200-184641200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:184637400-184639400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:184637600-184638800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:184637800-184638400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:184637800-184638800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:184637800-184639000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:184638000-184642800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:184638200-184638400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:184638200-184638600	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:184638200-184638800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:184638200-184638800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:184638200-184640400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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