Variant report

Variant	rs1770998
Chromosome Location	chr14:104541169-104541170
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104540844..104545973-chr14:104571339..104577117,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166183	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10134394	0.84[EUR][1000 genomes]
rs10135296	0.81[CEU][hapmap]
rs10135338	0.82[EUR][1000 genomes]
rs10135507	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[EUR][1000 genomes]
rs10137997	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs10139271	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10139483	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10144682	0.85[EUR][1000 genomes]
rs10147923	0.80[GIH][hapmap];0.83[EUR][1000 genomes]
rs10149233	0.84[EUR][1000 genomes]
rs10149351	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10149630	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10467890	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs10782497	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11160773	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11160778	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]
rs11160779	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[EUR][1000 genomes]
rs11160780	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11160783	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]
rs11160784	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11623042	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11625083	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626187	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11626960	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11627072	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11628540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11628592	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11628717	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]
rs11851441	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11851723	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs12100528	0.82[CEU][hapmap]
rs12147460	0.80[GIH][hapmap]
rs12147936	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12589388	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12589390	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885482	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12886010	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890969	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12895187	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12896676	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]
rs1744263	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1744266	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770997	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2146241	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208431	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs2263014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273842	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];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28377615	0.85[EUR][1000 genomes]
rs28391043	0.83[EUR][1000 genomes]
rs28505294	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28522352	0.83[EUR][1000 genomes]
rs28592598	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28644198	0.85[EUR][1000 genomes]
rs28725314	0.84[EUR][1000 genomes]
rs2887389	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4900604	0.80[GIH][hapmap]
rs4900607	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4900608	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4906389	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4906391	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906395	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4906397	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4906399	0.83[EUR][1000 genomes]
rs4906402	0.81[CEU][hapmap]
rs4906408	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4906409	0.85[EUR][1000 genomes]
rs55938939	0.83[EUR][1000 genomes]
rs61244535	0.85[EUR][1000 genomes]
rs6576017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143739	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7144813	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7145703	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7147107	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7149412	0.81[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs7150461	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7152856	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154082	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7156122	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158223	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7160557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7161468	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72714909	0.84[EUR][1000 genomes]
rs72714937	0.88[EUR][1000 genomes]
rs74089113	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003075	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008510	0.81[JPT][hapmap]
rs8010286	0.85[CEU][hapmap];0.80[GIH][hapmap];0.83[EUR][1000 genomes]
rs877009	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9285602	0.80[GIH][hapmap]
rs9324068	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs9324069	0.80[GIH][hapmap]
rs9671921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944163	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
9	esv1806632	chr14:104516262-104640011	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
10	nsv427946	chr14:104522565-104680785	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv518521	chr14:104523839-104545285	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv902325	chr14:104523839-104624689	Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv902326	chr14:104523839-104627198	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
14	nsv902327	chr14:104523839-104630711	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
15	nsv902328	chr14:104523839-104646326	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
16	nsv902329	chr14:104523839-104656659	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv902330	chr14:104523839-104662533	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
18	nsv902331	chr14:104523839-104849219	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
19	nsv1044920	chr14:104528663-104803058	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv902332	chr14:104534574-104646326	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1770998	TDRD9	cis	cerebellum	SCAN
rs1770998	TDRD9	cis	multi-tissue	Pritchard
rs1770998	C14orf180	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104540800-104541200	Weak transcription	Primary B cells from peripheral blood	blood

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