Variant report

Variant	rs7711420
Chromosome Location	chr5:178482994-178482995
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178482671..178485018-chr5:178485499..178487463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177932	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10479519	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479520	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516149	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10516150	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11505147	0.82[ASN][1000 genomes]
rs11951738	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957976	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958355	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11960161	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152869	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13160086	0.85[ASN][1000 genomes]
rs13161528	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13188724	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13359549	0.88[ASN][1000 genomes]
rs13359570	0.88[ASN][1000 genomes]
rs13359572	0.86[ASN][1000 genomes]
rs13361077	0.88[ASN][1000 genomes]
rs17078988	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17078991	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047354	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132671	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132672	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34054398	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34431447	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34881171	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35568336	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797615	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4700780	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs4700781	0.88[ASN][1000 genomes]
rs4701030	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4701045	0.87[ASN][1000 genomes]
rs58827878	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60061283	0.89[ASN][1000 genomes]
rs60073676	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393072	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393074	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393075	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393076	0.95[ASN][1000 genomes]
rs6601007	0.94[CEU][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6601010	0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6859576	0.94[ASN][1000 genomes]
rs6859767	0.92[ASN][1000 genomes]
rs6860309	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861539	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867119	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6867208	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868893	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6875473	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875622	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880315	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6888539	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6888567	0.84[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs6890317	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6891216	1.00[JPT][hapmap]
rs7707587	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708743	0.92[ASN][1000 genomes]
rs7709054	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732719	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7733072	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[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	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7711420	ZNF454	cis	parietal	SCAN
rs7711420	MXD3	cis	parietal	SCAN
rs7711420	RAB24	cis	parietal	SCAN
rs7711420	LOC345462	cis	multi-tissue	Pritchard
rs7711420	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178481000-178483600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr5:178481400-178483600	Enhancers	Placenta	Placenta
3	chr5:178482200-178483800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:178482400-178483400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:178482600-178483000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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