Variant report

Variant	rs6674145
Chromosome Location	chr1:186547333-186547334
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	chr1:186488450..186491951-chr1:186545141..186547515,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273198	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10489396	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs10489397	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10911877	0.82[JPT][hapmap]
rs10911899	0.82[EUR][1000 genomes]
rs1108635	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11799322	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11800288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11800338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11800651	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11801527	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11801617	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11802553	0.83[EUR][1000 genomes]
rs11802705	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803944	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11803969	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11804161	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11804785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11805289	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11805597	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11806017	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11806304	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11806329	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11806663	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11806701	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807318	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807443	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808165	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11808643	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11808900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11809088	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11809402	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11810534	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11811047	0.83[EUR][1000 genomes]
rs11811259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11811260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11811320	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11811335	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12239058	0.82[EUR][1000 genomes]
rs12723621	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12726528	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12726764	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731288	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731687	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12734267	0.83[EUR][1000 genomes]
rs12734420	0.83[EUR][1000 genomes]
rs12739006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739643	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12742751	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12747113	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12747991	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12750686	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12752376	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12753223	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12754662	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16825361	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16825403	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16825434	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16825473	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16825519	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16825521	0.86[AFR][1000 genomes]
rs16825600	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16825639	0.82[EUR][1000 genomes]
rs16825646	0.82[EUR][1000 genomes]
rs16825671	0.83[EUR][1000 genomes]
rs16825681	0.83[EUR][1000 genomes]
rs16825687	0.83[EUR][1000 genomes]
rs1883650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1883651	0.83[EUR][1000 genomes]
rs1883652	0.82[EUR][1000 genomes]
rs2008704	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2206974	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2223783	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2383384	0.84[AFR][1000 genomes]
rs2383509	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2383512	0.89[EUR][1000 genomes]
rs2383513	0.91[EUR][1000 genomes]
rs2383514	0.91[EUR][1000 genomes]
rs2891249	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2891250	0.82[EUR][1000 genomes]
rs33963275	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33996079	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34200789	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34228564	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34249733	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34272627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34310508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34365031	0.82[EUR][1000 genomes]
rs34459464	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34513409	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34578387	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34778311	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34781399	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34783173	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34858233	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35205448	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35206897	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35240980	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35326401	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35461575	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35481005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35636342	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35868587	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35945739	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36016361	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36030781	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36053737	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766698	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs3901243	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3933210	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4140432	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4140434	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4511065	0.82[EUR][1000 genomes]
rs4648292	1.00[YRI][hapmap]
rs5278	0.88[YRI][hapmap]
rs58626385	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6677346	0.82[JPT][hapmap]
rs6678198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678793	0.86[AFR][1000 genomes]
rs6680055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6682896	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6683271	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6701581	0.86[AFR][1000 genomes]
rs71516963	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71634161	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71634164	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71634167	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71634173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71634175	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71634176	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71634178	0.82[EUR][1000 genomes]
rs71634179	0.82[EUR][1000 genomes]
rs71634186	0.83[EUR][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6674145	C1orf14	cis	parietal	SCAN
rs6674145	OCLM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186545400-186548000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:186546600-186547800	Enhancers	Stomach Mucosa	stomach
3	chr1:186546600-186548000	Weak transcription	HMEC	breast
4	chr1:186546800-186548800	Enhancers	Esophagus	oesophagus
5	chr1:186547000-186547600	Weak transcription	Gastric	stomach
6	chr1:186547000-186548000	Weak transcription	Aorta	Aorta
7	chr1:186547200-186547800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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