Variant report

Variant	rs1685541
Chromosome Location	chr8:89472395-89472396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10088444	0.83[ASN][1000 genomes]
rs10283316	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10481112	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10504860	1.00[CEU][hapmap]
rs1094206	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955586	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155798	0.82[ASN][1000 genomes]
rs12156301	0.87[ASN][1000 genomes]
rs12548636	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12681181	0.87[EUR][1000 genomes]
rs12682164	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13251103	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1386767	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1394514	0.91[CEU][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1394517	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1394518	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394519	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1463923	0.87[ASN][1000 genomes]
rs1504797	0.87[EUR][1000 genomes]
rs1504804	0.91[CEU][hapmap]
rs1601818	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1601819	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1601820	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1601821	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1617649	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685549	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685551	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685553	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685554	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685559	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16882450	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1700154	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1700155	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857753	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1857754	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1857755	0.85[ASN][1000 genomes]
rs1875904	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134962	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134964	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2656311	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2656312	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28417952	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28705947	0.84[ASN][1000 genomes]
rs3105405	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105406	1.00[ASN][1000 genomes]
rs3105407	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105409	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110414	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110415	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110416	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110417	0.99[ASN][1000 genomes]
rs4246112	0.87[CEU][hapmap];0.83[ASN][1000 genomes]
rs4246113	0.87[CEU][hapmap];0.83[ASN][1000 genomes]
rs4246115	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4275260	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4305946	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4320597	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4395936	0.85[ASN][1000 genomes]
rs4434662	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4483202	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4515601	0.91[CEU][hapmap];0.85[ASN][1000 genomes]
rs4548227	0.85[ASN][1000 genomes]
rs4625076	0.91[CEU][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4961086	0.85[ASN][1000 genomes]
rs4961087	0.91[CEU][hapmap];0.85[ASN][1000 genomes]
rs4961090	0.85[ASN][1000 genomes]
rs4961093	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4961094	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961096	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56084092	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56187488	0.87[ASN][1000 genomes]
rs6989866	0.87[ASN][1000 genomes]
rs7009149	0.85[ASN][1000 genomes]
rs7828497	0.85[ASN][1000 genomes]
rs7834603	0.90[EUR][1000 genomes]
rs7835845	0.85[ASN][1000 genomes]
rs7838159	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821100	0.97[ASN][1000 genomes]
rs821111	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821114	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821117	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs821118	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821119	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs821120	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821121	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866592	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9656892	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv891172	chr8:89439469-89640705	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1685541	MMP16	cis	Skin Sun Exposed Lower leg	GTEx
rs1685541	MMP16	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89470200-89472600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
2	chr8:89471000-89472600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr8:89471600-89472400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:89471600-89472600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr8:89471600-89472600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr8:89471800-89472400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:89472000-89472800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr8:89472200-89472800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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