Variant report

Variant	rs576963
Chromosome Location	chr18:13145264-13145265
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	STAT3	chr18:13144937-13145266	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000267656	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10221326	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10221384	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs11080620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11663049	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12605638	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12954256	0.92[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap]
rs12955780	0.88[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1474043	0.92[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1786263	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1786270	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1786279	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1787000	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1787003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1787004	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1787008	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1973779	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28619103	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28641764	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2902856	0.94[CHD][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35790309	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3809912	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap]
rs472702	0.92[CEU][hapmap];0.86[MEX][hapmap]
rs472992	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs473580	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs474337	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs475139	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478006	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4797730	0.92[YRI][hapmap]
rs482360	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs482577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490853	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs491349	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs492458	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492723	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs498685	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs518145	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs527839	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs529620	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs529954	1.00[YRI][hapmap]
rs547084	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs554719	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs554854	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs556371	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs556536	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs557846	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs562151	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs565832	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs567031	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs569453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs570505	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs578208	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6505775	0.81[EUR][1000 genomes]
rs6505776	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6505777	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6505780	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs692833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692964	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71353243	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7226616	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7229870	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7233600	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7233814	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7234094	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7234960	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7236162	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237236	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7241536	0.84[CHB][hapmap]
rs7243660	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8088313	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs8089123	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs8097038	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8097125	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9783859	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9783903	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9949589	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9949682	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs9961669	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9964466	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
9	esv3437323	chr18:13141552-13145850	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1834772	chr18:13143415-13157966	Weak transcription ZNF genes & repeats Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1837050	chr18:13143415-13157966	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1842163	chr18:13143415-13157966	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv1803268	chr18:13143415-13175903	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs576963	CEP192	cis	Adipose Subcutaneous	GTEx
rs576963	CEP192	cis	multi-tissue	Pritchard
rs576963	CEP192	cis	Stomach	GTEx
rs576963	CEP192	cis	parietal	SCAN
rs576963	CEP192	cis	Heart Left Ventricle	GTEx
rs576963	CEP192	cis	Artery Aorta	GTEx
rs576963	CEP192	cis	Artery Tibial	GTEx
rs576963	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs576963	CEP192	cis	cerebellum	SCAN
rs576963	CEP192	cis	Esophagus Muscularis	GTEx
rs576963	CEP192	cis	Nerve Tibial	GTEx
rs576963	CEP192	cis	Thyroid	GTEx
rs576963	CEP192	cis	Temporal Cortex	GTEx
rs576963	CEP192	cis	Whole Blood	GTEx
rs576963	CEP192	cis	Brain Pons	GTEx
rs576963	CEP192	cis	lung	GTEx
rs576963	CEP192	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13136400-13145800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:13144600-13147200	Weak transcription	Thymus	Thymus
3	chr18:13144800-13151600	Weak transcription	Psoas Muscle	Psoas
4	chr18:13145200-13147200	Weak transcription	Adipose Nuclei	Adipose
5	chr18:13145200-13148600	Enhancers	HepG2	liver

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