Variant report

Variant	rs4305946
Chromosome Location	chr8:89431766-89431767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:89425784..89429285-chr8:89429819..89432091,4	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10088444	0.85[ASN][1000 genomes]
rs10283316	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10481112	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1094206	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955586	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12155796	0.90[AMR][1000 genomes]
rs12155798	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12156301	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12548636	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12682164	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13251103	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386767	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1394514	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1394517	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394518	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1394519	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1463923	0.88[ASN][1000 genomes]
rs1504797	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1601818	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1601819	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1601820	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1601821	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1617649	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685541	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1685549	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685551	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685553	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685554	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685559	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16882450	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1700150	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1700154	0.95[ASN][1000 genomes]
rs1700155	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1857753	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1857754	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1857755	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875904	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2134962	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2134964	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656311	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656312	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28417952	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28705947	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105405	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105406	0.99[ASN][1000 genomes]
rs3105407	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105409	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3110414	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3110415	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3110416	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3110417	0.97[ASN][1000 genomes]
rs4246112	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4246113	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4246115	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4275260	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4320597	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395936	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4434662	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4483202	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4515601	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4548227	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4625076	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961086	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961087	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961090	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961093	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4961094	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961096	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56084092	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56187488	0.88[ASN][1000 genomes]
rs6989866	0.88[ASN][1000 genomes]
rs7009149	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7014590	0.81[ASN][1000 genomes]
rs7828497	0.86[ASN][1000 genomes]
rs7834603	0.80[EUR][1000 genomes]
rs7835845	0.86[ASN][1000 genomes]
rs7838159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821100	0.96[ASN][1000 genomes]
rs821111	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821114	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821117	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821118	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs821119	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821120	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821121	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs866592	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656892	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv891171	chr8:89342944-89439469	Enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1019671	chr8:89393818-89443392	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1029978	chr8:89396644-89443392	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4305946	MMP16	cis	lung	GTEx
rs4305946	MMP16	cis	Thyroid	GTEx
rs4305946	MMP16	cis	Adipose Subcutaneous	GTEx
rs4305946	MMP16	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89427200-89432800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr8:89427200-89434000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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