Variant report

Variant	rs10954061
Chromosome Location	chr7:124626991-124626992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124625632..124627676-chr7:124628734..124631039,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1020629	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs10256073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10266152	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10281773	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1031952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs10500102	0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap]
rs10954064	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11761435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap]
rs11767519	0.87[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap]
rs11768553	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs11770818	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs11771004	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap]
rs11772420	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs11978268	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1248737	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs12532038	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs12537983	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs12539481	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12706625	1.00[ASW][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap]
rs12706627	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs13240050	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1404897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs1471570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1481334	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552116	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs1552117	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs17147723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17147889	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap]
rs2101100	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2127968	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2127969	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2127970	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291207	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs2402761	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28820412	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929322	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap]
rs2968868	0.85[EUR][1000 genomes]
rs34246481	0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs4360236	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4501522	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs612391	0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap]
rs627823	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs650653	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs651988	0.87[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs663056	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap]
rs664062	0.87[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap]
rs6946962	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs6965957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6966054	0.85[CHB][hapmap]
rs719974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs727521	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73432439	0.85[ASN][1000 genomes]
rs7784168	0.87[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7786989	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7787570	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7787804	0.87[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap]
rs7791488	0.88[YRI][hapmap]
rs7794637	0.87[ASW][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap]
rs7797011	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7811124	1.00[CEU][hapmap]
rs967297	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9785002	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs9942625	0.86[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1016655	chr7:124575684-124684279	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1032336	chr7:124590688-124673373	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1025873	chr7:124591433-124668423	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2761363	chr7:124591433-124673373	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1034654	chr7:124591433-124673373	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3380482	chr7:124593050-124628896	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv889139	chr7:124600505-124767295	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv608343	chr7:124610346-124674022	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10954061	POT1	cis	cerebellum	SCAN
rs10954061	IMPDH1	cis	cerebellum	SCAN
rs10954061	POT1	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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