Variant report

Variant	rs4276913
Chromosome Location	chr1:155131673-155131674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155131530..155134967-chr1:155138392..155140574,4	MCF-7	breast:
2	chr1:154955777..154957293-chr1:155130260..155131769,2	MCF-7	breast:
3	chr1:155066341..155068339-chr1:155131182..155134101,2	MCF-7	breast:
4	chr1:155098499..155102603-chr1:155131251..155133761,5	MCF-7	breast:
5	chr1:155106324..155115462-chr1:155131611..155142074,22	MCF-7	breast:
6	chr1:155112436..155115109-chr1:155129584..155132242,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169241	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000160688	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001848	0.85[JPT][hapmap]
rs10157801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908454	0.85[JPT][hapmap]
rs10908455	0.85[JPT][hapmap]
rs10908456	0.85[JPT][hapmap]
rs10908458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264306	0.85[JPT][hapmap]
rs11264314	0.82[JPT][hapmap]
rs11264319	0.85[JPT][hapmap]
rs11264329	0.85[JPT][hapmap]
rs11264333	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264337	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs11264338	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs11264339	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs11799962	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12028043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040970	0.85[JPT][hapmap]
rs12124306	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12127609	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145362	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs12752585	0.82[ASN][1000 genomes]
rs12904	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1462855	0.85[JPT][hapmap]
rs1870939	0.85[JPT][hapmap]
rs2066981	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs2306124	0.85[JPT][hapmap]
rs34257409	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765087	0.85[JPT][hapmap]
rs3766916	0.85[JPT][hapmap]
rs3814316	0.86[CHB][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs4072037	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs4246529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4276914	0.82[ASN][1000 genomes]
rs4390169	0.94[ASN][1000 genomes]
rs4421576	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4460629	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4644481	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4745	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4845407	0.85[JPT][hapmap]
rs4845408	0.85[JPT][hapmap]
rs4971052	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4971054	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4971059	0.85[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.92[AMR][1000 genomes]
rs4971066	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4971073	0.92[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.80[ASN][1000 genomes]
rs4971076	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971079	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4971085	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4971088	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4971091	0.89[AMR][1000 genomes]
rs4971093	0.96[AMR][1000 genomes]
rs6427158	0.85[JPT][hapmap]
rs6665822	0.85[JPT][hapmap]
rs6676150	0.94[ASN][1000 genomes]
rs6693477	0.85[JPT][hapmap]
rs7364524	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365544	0.85[JPT][hapmap]
rs7367207	0.85[JPT][hapmap]
rs7367897	0.85[JPT][hapmap]
rs7368345	0.85[JPT][hapmap]
rs7534162	0.85[JPT][hapmap]
rs7548955	0.82[JPT][hapmap]
rs7556304	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs914615	0.84[CHB][hapmap]
rs9297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
7	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
9	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
10	nsv946410	chr1:155119039-155135318	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4276913	SMCP	cis	cerebellum	SCAN
rs4276913	SLC39A1	cis	parietal	SCAN
rs4276913	ADAM15	cis	multi-tissue	Pritchard
rs4276913	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155131400-155132200	Enhancers	Placenta	Placenta
2	chr1:155131400-155132600	Enhancers	HepG2	liver

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