Variant report

Variant	rs1509424
Chromosome Location	chr9:108597879-108597880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10114077	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10116066	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117187	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10118661	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10121208	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10122308	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10156569	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10156571	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10217508	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10441744	0.81[EUR][1000 genomes]
rs10512340	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10512341	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739213	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10759128	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10759132	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10759133	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10759135	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10759143	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759145	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759146	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816294	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10816295	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10816296	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10816297	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10816298	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs10816299	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816300	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816302	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816308	0.80[EUR][1000 genomes]
rs10816310	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816311	0.80[EUR][1000 genomes]
rs10816313	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs10816314	0.82[EUR][1000 genomes]
rs10816319	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816324	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10816330	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10816331	0.81[EUR][1000 genomes]
rs10816337	0.81[EUR][1000 genomes]
rs10816345	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816346	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978196	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10978202	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10978203	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10978220	0.82[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10978226	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10978230	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10978235	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10978239	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10978240	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10978241	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10978251	0.81[EUR][1000 genomes]
rs10978252	0.81[EUR][1000 genomes]
rs10978253	0.80[EUR][1000 genomes]
rs10978257	0.81[EUR][1000 genomes]
rs10978265	0.81[EUR][1000 genomes]
rs10978300	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978301	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978302	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978303	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978306	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11506857	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11506858	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12338812	0.80[EUR][1000 genomes]
rs12338851	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12341846	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12344129	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12345343	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12346407	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347783	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12684672	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs13286237	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13301124	0.80[EUR][1000 genomes]
rs1979992	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1979993	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2136410	0.80[EUR][1000 genomes]
rs2175121	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2175122	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2271246	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2417621	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2900400	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010415	0.91[CHB][hapmap]
rs3105991	0.91[CHB][hapmap]
rs3817141	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4292753	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4563949	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477455	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6477460	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6477462	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6477463	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6477469	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477470	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477472	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477473	0.92[ASN][1000 genomes]
rs6477474	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7020523	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7024111	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024357	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024988	0.87[CHB][hapmap]
rs7026814	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7026968	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7028906	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7030236	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031360	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7031431	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7043222	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7046212	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7046293	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7047678	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7861268	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862565	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7865672	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7872125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7873663	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7875434	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs872245	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs872246	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9777628	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9969715	0.91[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1509424	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108596400-108599400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:108596600-108600000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr9:108597200-108598400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:108597400-108598400	Enhancers	Psoas Muscle	Psoas
5	chr9:108597400-108598600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:108597400-108598600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr9:108597400-108600000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:108597400-108600000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:108597600-108598000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:108597600-108598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:108597800-108599000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:108597800-108599800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr9:108597800-108600400	Enhancers	Ovary	ovary

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