Variant report

Variant	rs10978303
Chromosome Location	chr9:108592944-108592945
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108591234..108593447-chr9:108594377..108596340,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10114077	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10116066	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117187	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10118661	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs10121208	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10122308	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10156569	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10156571	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10512340	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs10512341	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739213	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10759128	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs10759132	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10759133	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs10759135	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10759143	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759144	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759145	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10759146	0.86[ASN][1000 genomes]
rs10816294	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10816295	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs10816296	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10816297	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10816298	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10816299	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10816300	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10816302	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs10816310	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10816313	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs10816319	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10816324	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10816345	0.81[AMR][1000 genomes];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]
rs10978196	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10978202	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10978203	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs10978220	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs10978226	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10978230	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10978235	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10978239	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10978240	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs10978241	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10978300	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978301	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978302	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978306	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11506857	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11506858	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338851	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12344129	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs12345343	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs12346407	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347783	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12348107	0.80[EUR][1000 genomes]
rs12348647	0.80[AMR][1000 genomes]
rs12684672	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs13286237	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1509424	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1979992	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1979993	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs2175121	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs2175122	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs2271246	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2417621	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900400	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010415	0.86[CHB][hapmap]
rs3105991	0.86[CHB][hapmap]
rs3817141	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs4292753	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563949	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477455	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6477460	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6477462	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs6477463	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs6477469	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477470	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477472	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477473	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477474	0.92[ASN][1000 genomes]
rs66993159	0.80[AMR][1000 genomes]
rs7020523	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7024111	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024357	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024988	0.82[CHB][hapmap]
rs7026814	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7026968	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs7028906	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs7030236	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031360	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs7031431	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7043222	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046212	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7046293	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7047678	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7861268	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7862565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865672	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs7872125	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873663	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7875434	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs872245	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872246	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9777628	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9969715	0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10978303	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL
rs10978303	C9orf125	cis	cerebellum	SCAN
rs10978303	TAL2	cis	cerebellum	SCAN
rs10978303	LPPR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108591400-108594800	Weak transcription	HMEC	breast

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