Variant report

Variant	rs6449480
Chromosome Location	chr5:59891782-59891783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11740327	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs11745627	0.85[ASN][1000 genomes]
rs1445852	0.94[ASN][1000 genomes]
rs1816899	0.82[ASN][1000 genomes]
rs187481	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs206789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409791	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs286153	0.81[GIH][hapmap];0.85[MEX][hapmap]
rs286154	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs286156	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs286158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4307050	0.90[CEU][hapmap]
rs4326096	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4515250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs4699959	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5012862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62373024	0.82[ASN][1000 genomes]
rs6449478	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6449484	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs6877561	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6896680	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6896942	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725028	0.92[AMR][1000 genomes]

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
rs6449480	ZSWIM6	cis	lymphoblastoid	seeQTL
rs6449480	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs6449480	DEPDC1B	cis	cerebellum	SCAN
rs6449480	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 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	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
6	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:59883400-59893600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:59883400-59894200	Weak transcription	Placenta	Placenta
10	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:59885000-59895800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:59885200-59895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:59885400-59894400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:59886600-59894400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:59888800-59893400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:59889000-59900800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:59889200-59900600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:59889200-59900800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:59889400-59893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:59889600-59893600	Weak transcription	Thymus	Thymus
23	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
24	chr5:59890400-59901600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:59890800-59892200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:59890800-59897600	Strong transcription	HepG2	liver
27	chr5:59891000-59893400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
29	chr5:59891200-59892400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:59891200-59894200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:59891200-59896400	Weak transcription	HUVEC	blood vessel
32	chr5:59891200-59909200	Weak transcription	HMEC	breast
33	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:59891400-59892000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:59891400-59892400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:59891400-59894400	Weak transcription	Fetal Lung	lung
37	chr5:59891600-59892000	Weak transcription	Primary T cells from cord blood	blood
38	chr5:59891600-59892800	Genic enhancers	Dnd41	blood

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