Variant report

Variant	rs889398
Chromosome Location	chr16:69556715-69556716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69555230..69558734-chr16:69596877..69599308,3	K562	blood:
2	chr16:69546010..69548545-chr16:69554522..69557315,2	K562	blood:
3	chr16:69554984..69557570-chr16:69599463..69601057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11640319	0.83[MKK][hapmap]
rs12599391	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs12923231	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12924872	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12929503	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12933292	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13330951	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs1364063	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437134	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs2032912	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2161630	0.84[MKK][hapmap]
rs244415	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs244417	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs244418	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs244420	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs35967356	0.93[EUR][1000 genomes]
rs3848278	0.86[MKK][hapmap]
rs4783721	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4783722	0.93[EUR][1000 genomes]
rs56096139	0.95[ASN][1000 genomes]
rs62052815	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62052816	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499240	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs6499244	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs669696	0.83[EUR][1000 genomes]
rs7187634	0.83[MKK][hapmap]
rs7191292	0.81[MKK][hapmap]
rs7192380	0.83[MKK][hapmap]
rs7359336	0.96[CEU][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs8049728	0.83[MKK][hapmap]
rs8055756	0.83[MKK][hapmap]
rs889399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs889398	MTSS1L	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69548200-69563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:69549200-69560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:69549600-69563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:69550000-69557000	Weak transcription	Placenta	Placenta
5	chr16:69552400-69563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:69554200-69556800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr16:69554600-69557000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr16:69555400-69561000	Weak transcription	A549	lung
9	chr16:69555600-69562600	Weak transcription	Hela-S3	cervix
10	chr16:69555800-69557200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr16:69555800-69558400	Enhancers	HepG2	liver
12	chr16:69555800-69560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:69555800-69561200	Weak transcription	HSMM	muscle
14	chr16:69555800-69563200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:69555800-69563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:69556200-69556800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr16:69556200-69563000	Weak transcription	NHEK	skin
18	chr16:69556200-69563200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:69556200-69563600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr16:69556400-69556800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr16:69556400-69557000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr16:69556400-69557200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:69556400-69560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:69556600-69556800	ZNF genes & repeats	GM12878-XiMat	blood
25	chr16:69556600-69556800	Flanking Active TSS	K562	blood

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