Variant report

Variant	rs13233234
Chromosome Location	chr7:147066163-147066164
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:147065836..147067829-chr7:147068950..147071013,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10500175	1.00[CHB][hapmap];0.93[MEX][hapmap]
rs10500179	0.82[MEX][hapmap]
rs10500185	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500187	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10952677	1.00[MEX][hapmap]
rs11763492	0.93[MEX][hapmap]
rs11764538	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769736	0.81[CEU][hapmap]
rs11770339	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772135	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs11773547	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs11773683	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12703911	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs12703916	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs12703921	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12703922	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs13221003	0.80[CEU][hapmap]
rs13221396	1.00[CEU][hapmap]
rs13221977	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs13222223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223092	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223171	0.93[MEX][hapmap]
rs13224673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13227291	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13229651	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13231364	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs13231991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13234094	1.00[CHB][hapmap]
rs13234757	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13235407	1.00[CHB][hapmap]
rs13235593	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238470	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13241063	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243643	0.91[EUR][1000 genomes]
rs13246604	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246788	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13247132	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247289	0.86[CEU][hapmap];0.82[AMR][1000 genomes]
rs1357896	1.00[CHB][hapmap];0.88[MEX][hapmap]
rs1404711	1.00[CHB][hapmap]
rs1406288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472361	0.93[MEX][hapmap]
rs1496544	0.87[MEX][hapmap]
rs1525227	0.80[EUR][1000 genomes]
rs1528520	1.00[ASN][1000 genomes]
rs17223460	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs17224658	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17412444	0.88[MEX][hapmap]
rs17498276	1.00[CHB][hapmap]
rs1842273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1842274	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871492	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046052	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2204412	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2373031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373128	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2373129	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs34163397	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34959888	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34993596	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35288063	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35594861	0.83[AMR][1000 genomes]
rs35696201	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756055	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894873	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894927	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36103173	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5028055	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6951143	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6957443	1.00[ASN][1000 genomes]
rs6979164	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs71530784	0.91[EUR][1000 genomes]
rs73473166	0.82[AMR][1000 genomes]
rs747138	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs7781303	0.83[AMR][1000 genomes]
rs7781464	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785125	0.83[AMR][1000 genomes]
rs7798078	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs7798162	0.81[CEU][hapmap]
rs7810103	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs872714	0.94[CEU][hapmap]
rs957484	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs997223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv933033	chr7:146720301-147081560	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1033898	chr7:146721499-147081768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv931005	chr7:146730472-147381257	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1033398	chr7:146989035-147101573	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
5	nsv465192	chr7:147001077-147086045	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
6	nsv608943	chr7:147001077-147086045	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13233234	ATP6V0E2	cis	cerebellum	SCAN
rs13233234	KCNH2	cis	parietal	SCAN
rs13233234	OR6W1P	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147065400-147066400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr7:147065400-147066600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:147065600-147066600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:147065800-147066200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:147065800-147066400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:147065800-147066800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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