Variant report

Variant	rs6477470
Chromosome Location	chr9:108589983-108589984
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10114077	0.82[AMR][1000 genomes]
rs10116066	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119128	0.82[AMR][1000 genomes]
rs10121208	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10121677	0.80[AMR][1000 genomes]
rs10121695	0.80[AMR][1000 genomes]
rs10123642	0.80[AMR][1000 genomes]
rs10125298	0.80[AMR][1000 genomes]
rs10156569	0.82[AMR][1000 genomes]
rs10156571	0.83[EUR][1000 genomes]
rs10217358	0.82[AMR][1000 genomes]
rs10512340	0.82[AMR][1000 genomes]
rs10512341	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759132	0.82[AMR][1000 genomes]
rs10759134	0.82[AMR][1000 genomes]
rs10759143	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759144	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759145	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10759146	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10816301	0.82[AMR][1000 genomes]
rs10816302	0.82[AMR][1000 genomes]
rs10816304	0.82[AMR][1000 genomes]
rs10816310	0.82[AMR][1000 genomes]
rs10816313	0.82[AMR][1000 genomes]
rs10816345	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816346	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816347	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978228	0.82[AMR][1000 genomes]
rs10978235	0.82[AMR][1000 genomes]
rs10978255	0.82[AMR][1000 genomes]
rs10978259	0.80[AMR][1000 genomes]
rs10978263	0.80[AMR][1000 genomes]
rs10978264	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10978267	0.80[AMR][1000 genomes]
rs10978300	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978301	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978302	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978303	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978306	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11506857	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11506858	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11532966	0.80[AMR][1000 genomes]
rs11562290	0.85[AMR][1000 genomes]
rs12001759	0.82[AMR][1000 genomes]
rs12003526	0.82[AMR][1000 genomes]
rs12339468	0.80[AMR][1000 genomes]
rs12344225	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12346407	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347783	0.82[AMR][1000 genomes]
rs12348107	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12348647	0.86[AMR][1000 genomes]
rs13283916	0.80[AMR][1000 genomes]
rs13286237	0.82[AMR][1000 genomes]
rs1509424	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2136406	0.80[AMR][1000 genomes]
rs2136407	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2136408	0.82[AMR][1000 genomes]
rs2175121	0.82[AMR][1000 genomes]
rs2175122	0.82[AMR][1000 genomes]
rs2417621	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900400	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35164306	0.82[AMR][1000 genomes]
rs3817141	0.82[AMR][1000 genomes]
rs4292753	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563949	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477453	0.82[AMR][1000 genomes]
rs6477454	0.82[AMR][1000 genomes]
rs6477462	0.82[AMR][1000 genomes]
rs6477463	0.82[AMR][1000 genomes]
rs6477464	0.82[AMR][1000 genomes]
rs6477466	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6477469	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477472	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477473	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477474	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66993159	0.83[AMR][1000 genomes]
rs67705477	0.80[AMR][1000 genomes]
rs7021727	0.82[AMR][1000 genomes]
rs7024111	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024357	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026814	0.82[AMR][1000 genomes]
rs7026968	0.82[AMR][1000 genomes]
rs7029064	0.80[AMR][1000 genomes]
rs7030236	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030399	0.82[AMR][1000 genomes]
rs7031360	0.82[AMR][1000 genomes]
rs7031431	0.82[AMR][1000 genomes]
rs7038788	0.82[AMR][1000 genomes]
rs7040532	0.82[AMR][1000 genomes]
rs7043222	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046947	0.80[AMR][1000 genomes]
rs73522059	0.80[AMR][1000 genomes]
rs7846853	0.82[AMR][1000 genomes]
rs7846993	0.82[AMR][1000 genomes]
rs7848176	0.82[AMR][1000 genomes]
rs7853483	0.82[AMR][1000 genomes]
rs7858663	0.82[AMR][1000 genomes]
rs7861268	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7862565	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862921	0.84[AMR][1000 genomes]
rs7867973	0.81[AMR][1000 genomes]
rs7871452	0.82[AMR][1000 genomes]
rs7871495	0.80[AMR][1000 genomes]
rs7872125	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873663	0.82[AMR][1000 genomes]
rs7874069	0.82[AMR][1000 genomes]
rs872245	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872246	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9777628	0.82[AMR][1000 genomes]
rs9969715	0.82[AMR][1000 genomes]
rs9987409	0.80[AMR][1000 genomes]
rs9987489	0.80[AMR][1000 genomes]
rs9987692	0.80[AMR][1000 genomes]
rs9987932	0.80[AMR][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	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv508558	chr9:108536115-108611087	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a
5	nsv1036849	chr9:108582944-108651205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6477470	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108585400-108590600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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