Variant report

Variant	rs12537685
Chromosome Location	chr7:103861035-103861036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103846910..103851184-chr7:103856864..103861366,6	MCF-7	breast:
2	chr7:103855618..103859131-chr7:103859954..103863291,3	MCF-7	breast:
3	chr7:103858966..103863231-chr7:103865702..103869473,3	K562	blood:

Variant related genes	Relation type
ENSG00000164815	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10227080	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10227508	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230891	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10231179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10231189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10236401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10239281	0.83[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs10242507	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246176	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256548	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256554	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265732	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10265960	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10265985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10269939	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1035168	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10953406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953407	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953409	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953410	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11973848	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11976032	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11980573	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11984388	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs12534723	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12535884	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537665	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12668873	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12669853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705177	0.87[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12705185	0.84[EUR][1000 genomes]
rs12705189	0.90[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs13223411	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223419	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13223492	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223504	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237931	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238019	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238105	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438174	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438176	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438761	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557663	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194836	0.87[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs194840	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs194842	0.87[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs194850	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs194853	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs194854	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs194856	0.83[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs194862	0.85[CEU][hapmap]
rs194863	0.83[CEU][hapmap]
rs194864	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs2058720	0.81[JPT][hapmap]
rs2058721	0.82[AMR][1000 genomes]
rs2075217	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2078807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2188284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2192965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214009	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299407	0.87[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs2307400	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2385139	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372965	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28681560	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842615	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28859908	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087358	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808011	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs3808012	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3808013	0.87[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs4006647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265123	0.88[YRI][hapmap]
rs4286867	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4370466	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4370467	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4445159	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4461829	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4486111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4529396	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4636136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729963	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4729971	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4729973	0.95[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4729974	0.91[MEX][hapmap]
rs55848	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs56669148	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487963	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944360	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs6946357	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946587	1.00[ASN][1000 genomes]
rs6948440	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948673	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948723	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6948967	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6952639	0.87[CEU][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs6962612	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6962673	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967816	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968451	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975834	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6979022	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs6979695	0.87[CEU][hapmap]
rs7350041	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs741325	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs756754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778396	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7795570	0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806228	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs9641322	0.83[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs9656092	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs971813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9791845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9918581	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9918639	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	nsv1029571	chr7:103855890-103909757	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv608066	chr7:103861035-103916484	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12537685	GPC2	cis	parietal	SCAN
rs12537685	ORAI2	cis	parietal	SCAN
rs12537685	TAF6	cis	parietal	SCAN
rs12537685	ATXN7L1	cis	cerebellum	SCAN
rs12537685	C7orf47	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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