Variant report

Variant	rs984509
Chromosome Location	chr5:59294872-59294873
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10044523	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10461664	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10805518	0.85[JPT][hapmap]
rs10940650	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10940651	0.82[EUR][1000 genomes]
rs1100918	0.84[JPT][hapmap]
rs11949422	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13154041	0.84[JPT][hapmap]
rs13164245	0.84[JPT][hapmap]
rs13164971	0.83[JPT][hapmap]
rs13173771	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1347401	0.88[JPT][hapmap]
rs1369285	0.88[JPT][hapmap]
rs1435071	0.96[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1435073	1.00[CEU][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1435079	0.92[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs1435080	0.88[JPT][hapmap]
rs1435083	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1435084	0.88[JPT][hapmap]
rs1508864	0.84[JPT][hapmap]
rs1529843	0.84[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs1544790	0.84[JPT][hapmap]
rs1583435	0.88[JPT][hapmap]
rs1588265	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs16890396	0.87[JPT][hapmap]
rs17315537	1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1983174	0.88[JPT][hapmap]
rs2016324	0.84[JPT][hapmap]
rs2548658	0.83[JPT][hapmap]
rs2548659	0.89[JPT][hapmap]
rs2662444	0.84[JPT][hapmap]
rs28427174	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28583371	0.96[EUR][1000 genomes]
rs28760347	0.96[EUR][1000 genomes]
rs2916868	0.81[EUR][1000 genomes]
rs3952631	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4476687	0.82[JPT][hapmap]
rs4547891	0.84[JPT][hapmap]
rs4699948	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4699949	0.88[JPT][hapmap]
rs4700349	1.00[JPT][hapmap]
rs4700354	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs4700355	0.84[JPT][hapmap]
rs62371491	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6449456	0.84[JPT][hapmap]
rs6872268	0.84[JPT][hapmap]
rs6885491	0.88[JPT][hapmap]
rs6889660	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6890036	0.84[CEU][hapmap]
rs6897766	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7379147	0.83[EUR][1000 genomes]
rs7379748	0.88[JPT][hapmap]
rs7703245	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs7715428	0.83[EUR][1000 genomes]
rs7719879	0.82[JPT][hapmap]
rs7731007	0.84[JPT][hapmap]
rs7734168	0.82[JPT][hapmap]
rs977417	0.83[CEU][hapmap]
rs981760	0.84[CEU][hapmap]
rs983280	0.80[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1027171	chr5:59267959-59340525	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs984509	MAP3K1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59283600-59298600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:59288000-59296600	Weak transcription	Aorta	Aorta
3	chr5:59291600-59296800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:59291800-59296200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59293400-59296000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:59294600-59295600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:59294800-59295200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:59294800-59295400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:59294800-59295400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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