Variant report

Variant	rs472163
Chromosome Location	chr9:94993123-94993124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94987677..94991575-chr9:94991944..94994722,3	K562	blood:
2	chr9:94991470..94993668-chr9:95052515..95055055,2	K562	blood:
3	chr9:94991849..94993766-chr9:94994920..94996657,2	MCF-7	breast:
4	chr9:94986649..94988919-chr9:94991898..94993516,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239183	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10125510	0.91[EUR][1000 genomes]
rs1058726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1058751	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10733744	0.93[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs10761159	0.91[EUR][1000 genomes]
rs1144933	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1152760	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1152761	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1152762	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1175737	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1175923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1175929	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1175930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1175931	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs11787696	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11788610	0.81[EUR][1000 genomes]
rs11789578	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11790257	0.89[ASN][1000 genomes]
rs11791931	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11792542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11793505	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11794966	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12001812	0.89[AFR][1000 genomes]
rs12555097	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2084289	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2398749	0.85[EUR][1000 genomes]
rs2761680	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs3894058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs41280213	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41280215	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743862	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4743864	0.89[ASN][1000 genomes]
rs4743866	0.93[CEU][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4743867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743868	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743871	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744123	0.89[ASN][1000 genomes]
rs4744124	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556155	0.93[CEU][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs557066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55894730	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56110031	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56308715	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56374228	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479421	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs7042199	0.91[EUR][1000 genomes]
rs72748400	0.81[EUR][1000 genomes]
rs72748402	0.81[EUR][1000 genomes]
rs7864453	0.91[EUR][1000 genomes]
rs895639	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409466	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9409467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409469	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];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409659	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409660	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409661	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409662	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409663	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9409665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409666	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs944949	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs472163	C9orf79	cis	parietal	SCAN
rs472163	ANKRD19	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94974000-94999000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:94982800-94993800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr9:94982800-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:94984000-95012400	Weak transcription	Stomach Mucosa	stomach
6	chr9:94985200-95001000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:94986000-95000600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:94988400-95000800	Weak transcription	Aorta	Aorta
9	chr9:94988800-95000400	Weak transcription	Fetal Heart	heart
10	chr9:94990000-94993400	Strong transcription	Brain Anterior Caudate	brain
11	chr9:94990200-94993600	Strong transcription	Adipose Nuclei	Adipose
12	chr9:94990200-94993600	Strong transcription	HepG2	liver
13	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:94990200-95004200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:94990200-95054000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:94990400-94993200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr9:94990400-94993200	Strong transcription	K562	blood
19	chr9:94990400-94993200	Strong transcription	NHEK	skin
20	chr9:94990400-94993400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:94990400-94993600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:94990400-94993600	Strong transcription	A549	lung
23	chr9:94990400-94994000	Strong transcription	Psoas Muscle	Psoas
24	chr9:94990400-94995800	Strong transcription	Primary B cells from cord blood	blood
25	chr9:94990400-94997800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr9:94990400-95004000	Strong transcription	Osteobl	bone
27	chr9:94990400-95004200	Strong transcription	NH-A	brain
28	chr9:94990400-95038200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:94990600-94994800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:94990600-94997600	Strong transcription	HSMM	muscle
31	chr9:94990600-95004000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:94991000-94996800	Weak transcription	Esophagus	oesophagus
33	chr9:94991000-95000400	Weak transcription	Colonic Mucosa	Colon
34	chr9:94991000-95007000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:94991200-94993400	Strong transcription	Liver	Liver
36	chr9:94991200-94993800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr9:94991200-94996000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:94991200-94996000	Weak transcription	Fetal Stomach	stomach
39	chr9:94991200-94996600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:94991200-94996800	Weak transcription	Spleen	Spleen
41	chr9:94991200-95000400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:94991200-95000400	Weak transcription	Pancreas	Pancrea
43	chr9:94991200-95002000	Weak transcription	Small Intestine	intestine
44	chr9:94991200-95006600	Strong transcription	HMEC	breast
45	chr9:94991200-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:94991200-95052400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:94991200-95053600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:94991400-94993600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:94991400-94994600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:94991400-94994600	Weak transcription	Muscle Satellite Cultured Cells	--

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