Variant report

Variant	rs2898287
Chromosome Location	chr5:59884233-59884234
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10043291	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10050803	0.88[CEU][hapmap]
rs10058456	0.86[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs10805370	0.85[CEU][hapmap]
rs10939856	0.81[ASN][1000 genomes]
rs10939860	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs10939862	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11739724	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740327	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11741754	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs11745627	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747927	0.83[ASN][1000 genomes]
rs11948543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11951503	0.92[ASN][1000 genomes]
rs11951950	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952735	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11955398	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs11956023	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11959922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12186391	0.81[EUR][1000 genomes]
rs12514253	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs12515025	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs12517174	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12517207	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs12522801	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs12655515	0.85[CEU][hapmap]
rs1379114	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs1379115	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs1379116	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1379117	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1444237	0.94[JPT][hapmap]
rs1445852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1456742	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1456743	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1460958	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs153152	0.82[ASN][1000 genomes]
rs1562235	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17387940	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs1816899	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1824120	0.82[EUR][1000 genomes]
rs1867702	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1870014	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs1992612	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs2045356	0.85[CEU][hapmap]
rs2061250	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs206789	0.86[CHB][hapmap]
rs2198865	0.89[ASN][1000 genomes]
rs2409792	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs248911	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248912	0.82[ASN][1000 genomes]
rs249070	0.95[ASN][1000 genomes]
rs2591636	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286154	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs286155	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs286156	0.85[ASN][1000 genomes]
rs286158	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3857236	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3958943	0.99[ASN][1000 genomes]
rs4277863	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs4524466	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4538567	0.84[EUR][1000 genomes]
rs4699959	0.88[ASN][1000 genomes]
rs4700378	0.91[ASN][1000 genomes]
rs4700379	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700380	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700381	0.85[ASN][1000 genomes]
rs5012862	0.92[ASN][1000 genomes]
rs55720622	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55768631	0.99[ASN][1000 genomes]
rs56137970	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56166952	0.95[ASN][1000 genomes]
rs56191602	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59155887	0.87[ASN][1000 genomes]
rs62372964	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62373024	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62373025	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6449483	0.86[CEU][hapmap]
rs6449493	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs6874072	0.85[CEU][hapmap]
rs6877561	0.85[ASN][1000 genomes]
rs6896942	0.90[ASN][1000 genomes]
rs755077	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs7707698	0.82[EUR][1000 genomes]
rs7719726	0.87[TSI][hapmap]
rs7720233	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs7736518	0.81[EUR][1000 genomes]
rs897672	0.96[CEU][hapmap]
rs9686489	0.81[EUR][1000 genomes]
rs9942410	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2898287	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 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	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59874600-59889600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
8	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:59876400-59890600	Weak transcription	Dnd41	blood
11	chr5:59879000-59886000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:59882200-59884600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:59882200-59890400	Weak transcription	Fetal Intestine Large	intestine
14	chr5:59882200-59890400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:59882200-59890800	Weak transcription	HepG2	liver
16	chr5:59883400-59893600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:59883400-59894200	Weak transcription	Placenta	Placenta

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