Variant report

Variant	rs3958943
Chromosome Location	chr5:59876749-59876750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10043291	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10058456	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs10939855	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10939856	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10939860	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10939862	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs11739724	0.94[ASN][1000 genomes]
rs11740327	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs11741754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11745627	0.86[ASN][1000 genomes]
rs11747927	0.82[ASN][1000 genomes]
rs11948543	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs11951503	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11951950	0.99[ASN][1000 genomes]
rs11952735	0.91[ASN][1000 genomes]
rs11955398	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs11956023	0.86[ASN][1000 genomes]
rs11959922	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12514253	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12515025	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12517174	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12517207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12522801	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1379114	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1379115	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1379116	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1379117	0.89[ASN][1000 genomes]
rs1444237	0.88[CEU][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs1456742	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1456743	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1460958	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]
rs153152	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1562235	0.99[ASN][1000 genomes]
rs17387940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1816899	0.83[ASN][1000 genomes]
rs1867702	0.88[ASN][1000 genomes]
rs1870014	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1992612	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs2061250	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs206789	0.86[CHB][hapmap]
rs2198865	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2409792	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs248911	0.81[ASN][1000 genomes]
rs248912	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs249070	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2591636	0.89[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs286154	0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs286155	0.89[ASN][1000 genomes]
rs286156	0.84[ASN][1000 genomes]
rs286158	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2898287	0.99[ASN][1000 genomes]
rs34417217	0.82[AMR][1000 genomes]
rs3857236	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs4277863	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs4504343	0.92[EUR][1000 genomes]
rs4524466	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4538566	0.92[EUR][1000 genomes]
rs4699959	0.89[ASN][1000 genomes]
rs4700378	0.91[ASN][1000 genomes]
rs4700379	0.93[ASN][1000 genomes]
rs4700380	0.93[ASN][1000 genomes]
rs4700381	0.85[ASN][1000 genomes]
rs5012862	0.92[ASN][1000 genomes]
rs55720622	0.84[ASN][1000 genomes]
rs55768631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56137970	0.96[ASN][1000 genomes]
rs56166952	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56191602	0.88[ASN][1000 genomes]
rs56347749	0.92[EUR][1000 genomes]
rs59155887	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62372964	0.98[ASN][1000 genomes]
rs62373023	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62373024	0.83[ASN][1000 genomes]
rs6449493	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs6874699	0.88[CEU][hapmap]
rs6877561	0.84[ASN][1000 genomes]
rs6896942	0.89[ASN][1000 genomes]
rs755077	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7704338	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs7719611	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs7720233	0.86[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs9942410	0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3958943	DEPDC1B	cis	cerebellum	SCAN
rs3958943	ELOVL7	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59881200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:59874600-59889600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
9	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:59875600-59878800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:59876400-59890600	Weak transcription	Dnd41	blood

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