Variant report

Variant	rs9971641
Chromosome Location	chr12:87765839-87765840
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	chr12:87765170..87767294-chr12:87767969..87769642,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10777039	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422458	0.99[ASN][1000 genomes]
rs4360774	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4409920	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491334	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512935	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4630369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643150	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4842457	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4842563	0.99[ASN][1000 genomes]
rs4842564	0.99[ASN][1000 genomes]
rs4842565	0.99[ASN][1000 genomes]
rs4842571	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55693604	0.99[ASN][1000 genomes]
rs55707841	0.99[ASN][1000 genomes]
rs55865225	0.99[ASN][1000 genomes]
rs56333727	0.99[ASN][1000 genomes]
rs57416479	0.99[ASN][1000 genomes]
rs58341223	0.99[ASN][1000 genomes]
rs60016330	0.99[ASN][1000 genomes]
rs60860693	0.99[ASN][1000 genomes]
rs66537815	0.99[ASN][1000 genomes]
rs67210764	0.99[ASN][1000 genomes]
rs67891841	0.99[ASN][1000 genomes]
rs7307618	0.99[ASN][1000 genomes]
rs7968573	0.99[ASN][1000 genomes]
rs7968713	0.99[ASN][1000 genomes]
rs7970629	0.99[ASN][1000 genomes]
rs9783446	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971644	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427918	chr12:87647585-87786660	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv430523	chr12:87757132-87865832	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv430525	chr12:87757132-87905532	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519837	chr12:87762364-87765839	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv438224	chr12:87762364-87773031	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9971641	GALNT4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87752400-87772200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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