Variant report

Variant	rs590666
Chromosome Location	chr9:79103366-79103367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1057406	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs1085341	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144923	0.86[ASN][1000 genomes]
rs11144926	0.80[AFR][1000 genomes]
rs11144929	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1969980	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs2282683	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs2476940	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476941	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745555	0.89[CHB][hapmap]
rs496253	0.83[ASN][1000 genomes]
rs503222	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553806	0.86[ASN][1000 genomes]
rs553927	0.86[ASN][1000 genomes]
rs566470	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570212	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs587111	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587171	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608697	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619429	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620295	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631887	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs634064	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664013	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs707739	0.80[JPT][hapmap]
rs785927	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590666	RFK	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
2	chr9:79080800-79117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:79081800-79117200	Weak transcription	Gastric	stomach
4	chr9:79082600-79117600	Weak transcription	NHLF	lung
5	chr9:79087600-79117400	Weak transcription	Colonic Mucosa	Colon
6	chr9:79089000-79103400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:79089000-79116400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:79091200-79108800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
10	chr9:79093600-79103600	Weak transcription	Fetal Thymus	thymus
11	chr9:79093600-79111400	Weak transcription	NHDF-Ad	bronchial
12	chr9:79093600-79117200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:79093800-79105400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:79093800-79109000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:79093800-79116600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:79093800-79117000	Weak transcription	HMEC	breast
17	chr9:79093800-79118000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:79094200-79120200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:79097000-79104000	Strong transcription	Fetal Intestine Small	intestine
20	chr9:79097200-79104000	Weak transcription	Small Intestine	intestine
21	chr9:79097200-79117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:79099200-79104000	Weak transcription	HSMM	muscle
23	chr9:79100600-79105400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:79100800-79105600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:79100800-79108000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:79101000-79106600	Enhancers	Stomach Mucosa	stomach
27	chr9:79101200-79105200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:79101200-79106800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr9:79101200-79116400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:79101400-79104600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:79101600-79106600	Enhancers	Primary B cells from peripheral blood	blood
32	chr9:79101600-79107600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:79101600-79108000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:79102200-79104400	Strong transcription	Osteobl	bone
35	chr9:79102200-79104600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:79102200-79104600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:79102200-79105600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr9:79102200-79111400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:79102400-79103800	Weak transcription	Fetal Intestine Large	intestine
40	chr9:79102600-79103800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:79102600-79103800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:79102600-79104800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:79102800-79103400	Weak transcription	Primary B cells from cord blood	blood
44	chr9:79102800-79103600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:79102800-79103800	Enhancers	Lung	lung
46	chr9:79102800-79107000	Weak transcription	Muscle Satellite Cultured Cells	--

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