Variant report

Variant	rs1504797
Chromosome Location	chr8:89434405-89434406
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	chr8:89432818..89434615-chr8:89434769..89436302,2	MCF-7	breast:
2	chr8:89428683..89430712-chr8:89432742..89436681,3	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10283316	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10481112	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1094206	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10955586	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12155798	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12156301	0.83[EUR][1000 genomes]
rs12548636	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12682164	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13251103	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1386767	0.82[EUR][1000 genomes]
rs1394514	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1394517	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1394518	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1394519	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1504804	0.87[CEU][hapmap]
rs1601818	0.85[EUR][1000 genomes]
rs1601819	0.83[EUR][1000 genomes]
rs1601820	0.83[EUR][1000 genomes]
rs1601821	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1617649	0.82[EUR][1000 genomes]
rs1685541	0.87[EUR][1000 genomes]
rs1685549	0.83[EUR][1000 genomes]
rs1685551	0.83[EUR][1000 genomes]
rs1685553	0.82[EUR][1000 genomes]
rs1685554	0.85[EUR][1000 genomes]
rs1685559	0.85[EUR][1000 genomes]
rs16882450	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1700150	0.83[EUR][1000 genomes]
rs1700155	0.84[EUR][1000 genomes]
rs1857753	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1857754	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1857755	0.81[AFR][1000 genomes]
rs1875904	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2134962	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2134964	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2656311	0.84[EUR][1000 genomes]
rs2656312	0.83[EUR][1000 genomes]
rs28417952	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28705947	0.84[EUR][1000 genomes]
rs3105405	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3105407	0.85[EUR][1000 genomes]
rs3105409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3110414	0.84[EUR][1000 genomes]
rs3110415	0.85[EUR][1000 genomes]
rs3110416	0.85[EUR][1000 genomes]
rs4246112	0.88[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs4246113	0.88[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs4246115	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4275260	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4305946	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4320597	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4395936	0.80[EUR][1000 genomes]
rs4434662	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4483202	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4515601	0.87[CEU][hapmap]
rs4548227	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4625076	0.83[EUR][1000 genomes]
rs4961086	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4961087	0.87[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4961093	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4961094	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961096	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56084092	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6989866	0.81[AFR][1000 genomes]
rs7009149	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7838159	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs821100	0.81[EUR][1000 genomes]
rs821111	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs821114	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs821117	0.85[EUR][1000 genomes]
rs821118	0.82[EUR][1000 genomes]
rs821119	0.83[EUR][1000 genomes]
rs821120	0.83[EUR][1000 genomes]
rs821121	0.83[EUR][1000 genomes]
rs866592	0.85[EUR][1000 genomes]
rs9656892	0.82[AFR][1000 genomes];0.82[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
rs1504797	MMP16	cis	Skin Sun Exposed Lower leg	GTEx
rs1504797	MMP16	cis	Adipose Subcutaneous	GTEx
rs1504797	MMP16	cis	Thyroid	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89432600-89435000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr8:89432600-89435200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr8:89432600-89435200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr8:89432800-89435000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr8:89433000-89437400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:89433800-89435200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr8:89433800-89436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:89434000-89435200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr8:89434400-89435200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links