Variant report

Variant	rs9561619
Chromosome Location	chr13:95188134-95188135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1408995	0.94[ASN][1000 genomes]
rs17181801	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17181808	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886787	0.91[ASN][1000 genomes]
rs1886789	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1891099	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1891100	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs2389132	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389133	0.91[ASN][1000 genomes]
rs2389134	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2389135	0.96[ASN][1000 genomes]
rs2389137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389138	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389139	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2892688	0.96[ASN][1000 genomes]
rs34536649	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35570210	0.89[ASN][1000 genomes]
rs4142020	0.96[ASN][1000 genomes]
rs4142021	0.96[ASN][1000 genomes]
rs4411370	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4442657	0.94[ASN][1000 genomes]
rs4553470	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492711	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492714	0.88[ASN][1000 genomes]
rs717769	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7317805	0.96[ASN][1000 genomes]
rs7318895	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7323407	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325171	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326382	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7327906	0.96[ASN][1000 genomes]
rs7329277	0.93[ASN][1000 genomes]
rs7330052	0.93[ASN][1000 genomes]
rs7330757	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7334113	0.92[ASN][1000 genomes]
rs7334290	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7334716	0.93[ASN][1000 genomes]
rs7334829	0.93[ASN][1000 genomes]
rs7335126	0.93[ASN][1000 genomes]
rs7336995	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7336997	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7337026	0.93[ASN][1000 genomes]
rs7337275	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7338715	0.96[ASN][1000 genomes]
rs7338730	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7490774	0.93[ASN][1000 genomes]
rs7492025	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs767925	0.96[ASN][1000 genomes]
rs7997227	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7998655	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8002991	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9284279	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301971	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9301972	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301973	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301974	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301975	0.94[ASN][1000 genomes]
rs9556376	0.91[ASN][1000 genomes]
rs9556377	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556378	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556379	0.91[ASN][1000 genomes]
rs9556380	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9556381	0.91[ASN][1000 genomes]
rs9556382	0.91[ASN][1000 genomes]
rs9556383	0.91[ASN][1000 genomes]
rs9556384	0.91[ASN][1000 genomes]
rs9556386	0.93[ASN][1000 genomes]
rs9556387	0.93[ASN][1000 genomes]
rs9556388	0.93[ASN][1000 genomes]
rs9556390	0.96[ASN][1000 genomes]
rs9556391	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556392	0.96[ASN][1000 genomes]
rs9556397	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556398	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561568	0.91[ASN][1000 genomes]
rs9561569	0.91[ASN][1000 genomes]
rs9561570	0.91[ASN][1000 genomes]
rs9561571	0.91[ASN][1000 genomes]
rs9561572	0.91[ASN][1000 genomes]
rs9561573	0.91[ASN][1000 genomes]
rs9561574	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561575	0.91[ASN][1000 genomes]
rs9561576	0.91[ASN][1000 genomes]
rs9561577	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9561578	0.93[ASN][1000 genomes]
rs9561579	0.91[ASN][1000 genomes]
rs9561580	0.93[ASN][1000 genomes]
rs9561581	0.93[ASN][1000 genomes]
rs9561582	0.92[ASN][1000 genomes]
rs9561583	0.93[ASN][1000 genomes]
rs9561584	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561588	0.93[ASN][1000 genomes]
rs9561589	0.94[ASN][1000 genomes]
rs9561591	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561592	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561593	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561595	0.96[ASN][1000 genomes]
rs9561596	0.96[ASN][1000 genomes]
rs9561597	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561599	0.96[ASN][1000 genomes]
rs9561600	0.96[ASN][1000 genomes]
rs9561601	0.96[ASN][1000 genomes]
rs9561602	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561603	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561604	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561605	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561606	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561620	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561621	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561622	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561623	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9561625	0.91[ASN][1000 genomes]
rs9561626	0.91[ASN][1000 genomes]
rs9590029	0.96[ASN][1000 genomes]
rs9590030	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv562756	chr13:95178317-95238154	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9561619	DCT	cis	parietal	SCAN
rs9561619	DCT	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95186800-95188200	Enhancers	Placenta	Placenta
2	chr13:95187000-95188200	Enhancers	Placenta Amnion	Placenta Amnion
3	chr13:95187400-95188600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr13:95187400-95188600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr13:95187400-95189600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:95187600-95188200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr13:95187600-95188600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr13:95187600-95188600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr13:95187600-95188600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr13:95187600-95188800	Enhancers	Primary T cells from cord blood	blood
11	chr13:95187600-95188800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr13:95187800-95188200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:95187800-95188200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr13:95187800-95188400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr13:95187800-95188400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr13:95187800-95188400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr13:95187800-95188600	Enhancers	Dnd41	blood
18	chr13:95188000-95188400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr13:95188000-95188400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr13:95188000-95188600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr13:95188000-95188600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:95188000-95188600	Enhancers	Fetal Thymus	thymus
23	chr13:95188000-95189200	Enhancers	Thymus	Thymus

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