Variant report

Variant	rs28705947
Chromosome Location	chr8:89410975-89410976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:89410966-89411057	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:89409309..89411257-chr8:89436132..89438369,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP272	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10283316	0.84[EUR][1000 genomes]
rs10481112	0.83[EUR][1000 genomes]
rs1094206	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10955586	0.82[EUR][1000 genomes]
rs12155796	0.84[AMR][1000 genomes]
rs12155798	0.86[AMR][1000 genomes]
rs12156301	0.82[AMR][1000 genomes]
rs12548636	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12682164	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13251103	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1386767	0.82[ASN][1000 genomes]
rs1394514	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394517	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1394518	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1394519	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1504797	0.84[EUR][1000 genomes]
rs1601818	0.81[ASN][1000 genomes]
rs1601819	0.82[ASN][1000 genomes]
rs1601820	0.82[ASN][1000 genomes]
rs1601821	0.82[ASN][1000 genomes]
rs1617649	0.82[ASN][1000 genomes]
rs1685541	0.84[ASN][1000 genomes]
rs1685549	0.82[ASN][1000 genomes]
rs1685551	0.82[ASN][1000 genomes]
rs1685553	0.82[ASN][1000 genomes]
rs1685554	0.82[ASN][1000 genomes]
rs1685559	0.82[ASN][1000 genomes]
rs16882450	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1700150	0.82[ASN][1000 genomes]
rs1700154	0.80[ASN][1000 genomes]
rs1700155	0.82[ASN][1000 genomes]
rs1857753	0.83[EUR][1000 genomes]
rs1857754	0.84[EUR][1000 genomes]
rs1875904	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2134962	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2134964	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656312	0.82[ASN][1000 genomes]
rs28417952	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3105405	0.84[ASN][1000 genomes]
rs3105406	0.84[ASN][1000 genomes]
rs3105407	0.84[ASN][1000 genomes]
rs3105409	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3110414	0.84[ASN][1000 genomes]
rs3110415	0.84[ASN][1000 genomes]
rs3110416	0.84[ASN][1000 genomes]
rs3110417	0.85[ASN][1000 genomes]
rs4246115	0.84[EUR][1000 genomes]
rs4275260	0.84[EUR][1000 genomes]
rs4305946	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4320597	0.82[EUR][1000 genomes]
rs4434662	0.84[EUR][1000 genomes]
rs4483202	0.84[EUR][1000 genomes]
rs4515601	0.80[EUR][1000 genomes]
rs4548227	0.80[EUR][1000 genomes]
rs4961093	0.83[EUR][1000 genomes]
rs4961094	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961096	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56084092	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7009149	0.81[EUR][1000 genomes]
rs7838159	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821100	0.81[ASN][1000 genomes]
rs821111	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs821114	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs821117	0.82[ASN][1000 genomes]
rs821118	0.81[ASN][1000 genomes]
rs821119	0.82[ASN][1000 genomes]
rs821120	0.84[ASN][1000 genomes]
rs821121	0.84[ASN][1000 genomes]
rs866592	0.82[ASN][1000 genomes]
rs9656892	0.81[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28705947	MMP16	cis	Thyroid	GTEx
rs28705947	MMP16	cis	Adipose Subcutaneous	GTEx
rs28705947	MMP16	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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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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