Variant report

Variant	rs477220
Chromosome Location	chr17:38541063-38541064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38537003..38538874-chr17:38538974..38542009,5	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1530363	0.81[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs1662574	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16965783	0.93[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2586112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2715556	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715557	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473198	1.00[ASW][hapmap];0.93[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs474510	0.83[EUR][1000 genomes]
rs505633	0.95[ASN][1000 genomes]
rs506728	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507564	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs510336	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517047	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs525217	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs525812	0.81[CEU][hapmap]
rs532299	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552857	0.81[EUR][1000 genomes]
rs557498	0.81[EUR][1000 genomes]
rs558068	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62066565	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs477220	MYO19	cis	cerebellum	SCAN
rs477220	KRT33B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38521400-38541800	Weak transcription	A549	lung
2	chr17:38523800-38546200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:38531400-38542600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38531400-38543800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:38531600-38543000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:38531600-38543400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:38531600-38544600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:38531600-38545000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr17:38531800-38544000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr17:38532600-38544400	Weak transcription	HSMM	muscle
11	chr17:38533400-38542400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr17:38533600-38542400	Weak transcription	Dnd41	blood
13	chr17:38533600-38549600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:38533800-38542200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:38533800-38544400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:38533800-38544400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:38534000-38543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:38535200-38546400	Weak transcription	Thymus	Thymus
19	chr17:38536000-38544000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr17:38536800-38562000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:38537200-38558600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:38537600-38544600	Weak transcription	K562	blood
23	chr17:38538000-38544000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:38538000-38544000	Weak transcription	HepG2	liver
25	chr17:38538200-38544600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:38538200-38557400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr17:38538400-38559200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:38538600-38545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr17:38538800-38544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:38539000-38544000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr17:38539200-38543400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:38539200-38544800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:38539400-38541400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:38539400-38542600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
36	chr17:38539600-38544000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:38539800-38543200	Weak transcription	HMEC	breast
38	chr17:38539800-38543600	Weak transcription	Fetal Intestine Small	intestine
39	chr17:38539800-38546200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:38540000-38544600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:38540000-38546200	Weak transcription	Fetal Stomach	stomach
42	chr17:38540200-38542200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:38540200-38542600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr17:38540200-38549000	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:38540200-38553000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
47	chr17:38540400-38553000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:38540600-38543800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:38540800-38544000	Weak transcription	GM12878-XiMat	blood
50	chr17:38540800-38544200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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