Variant report

Variant	rs11160783
Chromosome Location	chr14:104513387-104513388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:104513352-104513392	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104512280..104514281-chr14:104515580..104517286,2	MCF-7	breast:

Variant related genes	Relation type
TDRD9	TF binding region
ENSG00000156414	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10135296	0.81[CEU][hapmap]
rs10135507	0.85[CEU][hapmap]
rs10137997	0.81[CEU][hapmap]
rs10139271	0.85[ASN][1000 genomes]
rs10139483	0.85[ASN][1000 genomes]
rs10149351	0.84[ASN][1000 genomes]
rs10149630	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10467890	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11160773	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11160778	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11160779	0.85[CEU][hapmap]
rs11160780	0.81[CEU][hapmap]
rs11160784	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11623042	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11625083	0.87[ASN][1000 genomes]
rs11626187	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11626960	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11627072	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628540	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11628592	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628717	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11851441	0.84[CEU][hapmap]
rs11851723	0.90[CEU][hapmap]
rs12100528	0.82[CEU][hapmap]
rs12147936	0.85[CEU][hapmap]
rs12589388	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589390	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12885482	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12886010	0.83[ASN][1000 genomes]
rs12890969	0.84[ASN][1000 genomes]
rs12895187	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12896676	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1744263	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1744266	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1770997	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770998	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1771002	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2146241	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208431	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2263014	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273842	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28505294	0.84[ASN][1000 genomes]
rs28592598	0.80[ASN][1000 genomes]
rs2887389	0.87[ASN][1000 genomes]
rs4900607	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4900608	0.85[CEU][hapmap]
rs4906389	0.81[ASN][1000 genomes]
rs4906391	0.84[ASN][1000 genomes]
rs4906395	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[TSI][hapmap]
rs4906397	0.88[CEU][hapmap]
rs4906402	0.81[CEU][hapmap]
rs4906408	0.85[CEU][hapmap]
rs6576017	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7143739	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7145703	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7147107	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7149412	0.81[TSI][hapmap]
rs7150461	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152856	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154082	0.84[ASN][1000 genomes]
rs7156122	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7158223	0.81[CEU][hapmap]
rs7160557	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74089113	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8003075	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs8010286	0.85[CEU][hapmap]
rs877009	0.81[CEU][hapmap]
rs9324068	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs9671921	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
4	nsv1049690	chr14:104411621-104575838	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv542208	chr14:104411621-104575838	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526680	chr14:104427043-104568472	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1047990	chr14:104460605-104556463	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv542209	chr14:104497447-104540729	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1050479	chr14:104500427-104805738	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11160783	C14orf180	cis	cerebellum	SCAN
rs11160783	TDRD9	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104492200-104516000	Weak transcription	Spleen	Spleen
2	chr14:104496400-104520800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr14:104502800-104513400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:104509200-104520600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:104510600-104516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:104510800-104521000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:104511000-104514000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr14:104511800-104516200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr14:104512800-104515000	Weak transcription	Fetal Brain Male	brain

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