Variant report

Variant	rs206789
Chromosome Location	chr5:59903971-59903972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10939860	0.82[CHD][hapmap]
rs10939862	0.82[CHD][hapmap]
rs11740327	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11741754	0.82[CHD][hapmap]
rs11745627	0.89[ASN][1000 genomes]
rs11955398	0.82[CHD][hapmap]
rs11959922	0.81[CHB][hapmap]
rs12514253	0.82[CHD][hapmap]
rs12515025	0.82[CHD][hapmap]
rs12517174	0.82[CHD][hapmap]
rs12517207	0.82[CHD][hapmap]
rs1379114	0.82[CHD][hapmap]
rs1445852	0.83[ASN][1000 genomes]
rs17387940	0.82[CHD][hapmap]
rs1816899	0.86[ASN][1000 genomes]
rs1870014	0.82[CHD][hapmap]
rs187481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061250	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2409791	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2409792	0.82[CHD][hapmap]
rs286148	0.84[ASN][1000 genomes]
rs286153	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs286154	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs286156	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs286158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857236	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs4307050	0.90[CEU][hapmap]
rs4326096	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4515250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4524466	0.82[CHB][hapmap]
rs4699959	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5012862	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62373023	0.85[ASN][1000 genomes]
rs62373024	0.92[ASN][1000 genomes]
rs62373025	0.87[ASN][1000 genomes]
rs6449478	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6449480	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6449484	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs6877561	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6896680	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6896942	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7725028	0.89[AMR][1000 genomes]
rs9942410	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs206789	ZSWIM6	cis	lymphoblastoid	seeQTL
rs206789	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL
rs206789	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs206789	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
9	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
10	chr5:59891200-59909200	Weak transcription	HMEC	breast
11	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:59892000-59912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:59893000-59911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:59894000-59906000	Weak transcription	Osteobl	bone
15	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
16	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
17	chr5:59897600-59907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:59898800-59907200	Weak transcription	GM12878-XiMat	blood
19	chr5:59899000-59905800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:59899200-59910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:59899400-59907200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:59899400-59907600	Weak transcription	Dnd41	blood
23	chr5:59899400-59910800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:59899400-59912600	Weak transcription	Fetal Thymus	thymus
25	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:59899600-59907200	Weak transcription	K562	blood
27	chr5:59899600-59908600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:59899600-59909000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:59899600-59910000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:59899800-59924800	Weak transcription	HepG2	liver
31	chr5:59900000-59910600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:59901400-59906400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:59901600-59908600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:59901800-59911400	Weak transcription	Placenta	Placenta
35	chr5:59902200-59924800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:59903600-59907200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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