Variant report

Variant	rs11160778
Chromosome Location	chr14:104478740-104478741
allele	C/T
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	NR2F2	chr14:104478244-104478844	MCF-7	breast:	n/a	n/a
2	MAX	chr14:104478216-104478864	MCF-7	breast:	n/a	n/a
3	GATA3	chr14:104478286-104478912	MCF-7	breast:	n/a	n/a
4	TFAP2C	chr14:104478275-104478796	Hela-S3	cervix:	n/a	chr14:104478615-104478630
5	NFIC	chr14:104478284-104478819	ECC-1	luminal epithelium:	n/a	n/a
6	RFX5	chr14:104478442-104478859	Hela-S3	cervix:	n/a	n/a
7	TEAD4	chr14:104478434-104478861	ECC-1	luminal epithelium:	n/a	n/a
8	NR2F2	chr14:104478193-104478888	MCF-7	breast:	n/a	n/a
9	MYC	chr14:104478518-104478800	MCF10A-Er-Src	breast:	n/a	n/a
10	TEAD4	chr14:104478372-104478921	ECC-1	luminal epithelium:	n/a	n/a
11	TFAP2A	chr14:104478332-104478761	Hela-S3	cervix:	n/a	chr14:104478570-104478585
12	MAX	chr14:104478325-104478820	Hela-S3	cervix:	n/a	n/a
13	MAX	chr14:104478540-104478803	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr14:104478497-104478876	Hela-S3	cervix:	n/a	n/a
15	SMC3	chr14:104478517-104478766	Hela-S3	cervix:	n/a	n/a
16	HDAC2	chr14:104478271-104478897	MCF-7	breast:	n/a	chr14:104478853-104478867 chr14:104478849-104478863 chr14:104478854-104478868 chr14:104478852-104478866 chr14:104478855-104478869
17	GTF2F1	chr14:104478447-104478785	Hela-S3	cervix:	n/a	n/a
18	NFIC	chr14:104478367-104478952	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
RN7SL634P	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10132127	0.83[EUR][1000 genomes]
rs10132153	0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs10134394	0.82[EUR][1000 genomes]
rs10135296	0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[EUR][1000 genomes]
rs10135338	0.83[EUR][1000 genomes]
rs10135507	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10137997	0.84[EUR][1000 genomes]
rs10139271	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10139483	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10144682	0.83[EUR][1000 genomes]
rs10147923	0.83[EUR][1000 genomes]
rs10149233	0.84[EUR][1000 genomes]
rs10149351	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10149630	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10149734	0.81[EUR][1000 genomes]
rs10467890	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10782497	0.81[EUR][1000 genomes]
rs11160773	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11160777	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11160779	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11160780	0.83[EUR][1000 genomes]
rs11160783	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]
rs11160784	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11623042	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11625083	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11626187	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11626960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11627072	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628592	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628717	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851097	0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs11851441	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11851723	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12100528	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12147828	0.87[EUR][1000 genomes]
rs12147936	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12589388	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589390	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12885482	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12886010	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12890969	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12895187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896676	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744263	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1744266	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1770997	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1771002	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1957517	0.83[EUR][1000 genomes]
rs2146241	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2208431	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2263014	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273842	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28377615	0.83[EUR][1000 genomes]
rs28391043	0.83[EUR][1000 genomes]
rs28505294	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28522352	0.83[EUR][1000 genomes]
rs28592598	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28644198	0.83[EUR][1000 genomes]
rs28725314	0.84[EUR][1000 genomes]
rs2887389	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4900607	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900608	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4906389	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906391	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906392	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4906395	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906397	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4906399	0.83[EUR][1000 genomes]
rs4906401	0.87[EUR][1000 genomes]
rs4906402	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4906408	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4906409	0.83[EUR][1000 genomes]
rs55938939	0.84[EUR][1000 genomes]
rs61244535	0.83[EUR][1000 genomes]
rs61319604	0.87[EUR][1000 genomes]
rs6576017	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7143739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144813	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7145703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147107	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7149412	0.81[CHB][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7150461	0.92[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152856	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154082	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7156122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7158223	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs7160557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161468	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72712889	0.81[EUR][1000 genomes]
rs72714904	0.87[EUR][1000 genomes]
rs72714909	0.84[EUR][1000 genomes]
rs72714937	0.81[EUR][1000 genomes]
rs74089113	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8003075	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8008510	0.81[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs8009349	0.82[EUR][1000 genomes]
rs8010286	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs8022833	0.83[EUR][1000 genomes]
rs877009	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs9324068	0.85[CEU][hapmap]
rs9671921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9944163	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1048353	chr14:104361402-104483286	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11160778	TDRD9	cis	multi-tissue	Pritchard
rs11160778	TDRD9	cis	cerebellum	SCAN
rs11160778	C14orf180	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104473600-104495400	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr14:104474000-104491600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr14:104477200-104481600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr14:104478000-104479800	Enhancers	Hela-S3	cervix
5	chr14:104478200-104478800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr14:104478400-104478800	Enhancers	Left Ventricle	heart
7	chr14:104478400-104478800	Enhancers	Pancreas	Pancrea
8	chr14:104478400-104478800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr14:104478400-104478800	Enhancers	Right Atrium	heart
10	chr14:104478400-104479200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:104478400-104479800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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