Variant report

Variant	rs1918939
Chromosome Location	chr7:78902684-78902685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:78900547..78903338-chr7:78905670..78907338,2	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10225262	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10230177	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10232677	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10234403	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10235211	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10240268	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10241692	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10254948	0.83[EUR][1000 genomes]
rs10254950	0.82[JPT][hapmap]
rs10266537	1.00[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs10270040	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10270645	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10270764	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10273845	1.00[CEU][hapmap]
rs10480716	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10953797	1.00[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs10953806	0.82[EUR][1000 genomes]
rs10953812	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10953821	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953823	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953825	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10953826	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953827	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10953828	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10953835	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11535245	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11766918	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11768754	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11977493	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs12111592	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12111980	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12154356	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12154470	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12216581	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12532467	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12534590	1.00[CEU][hapmap]
rs12536811	0.83[AMR][1000 genomes]
rs12538685	0.82[AMR][1000 genomes]
rs12539220	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12540324	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12666243	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12706101	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12706102	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13221173	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13222018	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13224467	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13224739	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13230407	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13230579	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs13234027	0.81[AMR][1000 genomes]
rs13237396	0.83[EUR][1000 genomes]
rs13237397	0.83[EUR][1000 genomes]
rs13240307	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13243285	0.81[AMR][1000 genomes]
rs13243756	0.86[EUR][1000 genomes]
rs13306942	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1358473	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1406152	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1406157	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1406158	0.86[EUR][1000 genomes]
rs1406159	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs1528263	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1528265	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1528269	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1528270	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1528271	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs1528272	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1528273	0.86[EUR][1000 genomes]
rs1528274	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1528280	0.90[EUR][1000 genomes]
rs1528281	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554833	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1554834	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1554835	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes]
rs1554836	0.82[AMR][1000 genomes]
rs1881292	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs1918936	0.92[EUR][1000 genomes]
rs1918937	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1918938	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2058393	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2158708	0.82[JPT][hapmap]
rs2159709	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2190175	0.82[JPT][hapmap]
rs2242505	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2364902	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364913	0.82[JPT][hapmap]
rs2886212	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34059048	0.80[AMR][1000 genomes]
rs34066812	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34983504	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35035926	0.83[AMR][1000 genomes]
rs4129689	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4141208	0.82[JPT][hapmap]
rs4143262	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4256536	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4445162	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4727838	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4727841	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4727843	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4730746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730747	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60960798	0.87[EUR][1000 genomes]
rs62458964	0.82[AMR][1000 genomes]
rs62458973	0.83[EUR][1000 genomes]
rs6466593	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6466621	0.82[JPT][hapmap]
rs6946286	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6946789	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6947782	0.86[EUR][1000 genomes]
rs6950549	0.82[EUR][1000 genomes]
rs6952164	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6953483	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6953771	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs6961357	0.83[EUR][1000 genomes]
rs6965742	0.83[EUR][1000 genomes]
rs6968269	0.80[EUR][1000 genomes]
rs71531164	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs717067	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs7341488	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7455235	0.80[EUR][1000 genomes]
rs7459140	1.00[CEU][hapmap]
rs7779953	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7781907	0.82[EUR][1000 genomes]
rs7782460	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs7782585	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs7785706	0.82[JPT][hapmap]
rs7788509	0.82[JPT][hapmap]
rs7792796	0.82[JPT][hapmap]
rs7805028	0.81[EUR][1000 genomes]
rs7808561	0.82[JPT][hapmap]
rs949496	0.85[EUR][1000 genomes]
rs9648980	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs970491	0.82[JPT][hapmap]
rs9886146	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9886330	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969308	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv437988	chr7:78806100-78910974	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv831041	chr7:78819499-78973222	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1918939	TMEM120A	cis	cerebellum	SCAN
rs1918939	MAGI2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78896800-78911600	Weak transcription	Aorta	Aorta
2	chr7:78899400-78909600	Weak transcription	NHLF	lung
3	chr7:78900800-78903600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:78902000-78902800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:78902200-78902800	Enhancers	HUVEC	blood vessel
6	chr7:78902400-78910200	Weak transcription	Osteobl	bone
7	chr7:78902600-78911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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