Variant report

Variant	rs9889198
Chromosome Location	chr16:46890234-46890235
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46888367..46890662-chr16:46962617..46964242,2	MCF-7	breast:
2	chr16:46722100..46725335-chr16:46890075..46893189,3	K562	blood:

Variant related genes	Relation type
ENSG00000091651	Chromatin interaction
ENSG00000069329	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1009391	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934580	1.00[ASN][1000 genomes]
rs12935606	0.84[EUR][1000 genomes]
rs1641122	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869006	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354454	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4246381	1.00[ASN][1000 genomes]
rs4966706	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.84[EUR][1000 genomes]
rs56042735	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.83[EUR][1000 genomes]
rs57127559	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58074838	0.81[EUR][1000 genomes]
rs62057633	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186748	0.84[EUR][1000 genomes]
rs7196375	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.81[EUR][1000 genomes]
rs7197485	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053137	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058734	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1795793	chr16:46882046-46904119	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9889198	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46886200-46891200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr16:46886200-46891200	Weak transcription	Placenta	Placenta
3	chr16:46886200-46905600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:46886400-46893400	Weak transcription	Gastric	stomach
5	chr16:46887200-46891400	Weak transcription	Fetal Kidney	kidney
6	chr16:46887600-46896800	Enhancers	HepG2	liver
7	chr16:46888400-46891000	Weak transcription	Brain Hippocampus Middle	brain
8	chr16:46888400-46891000	Weak transcription	Brain Substantia Nigra	brain
9	chr16:46888400-46891200	Weak transcription	Brain Angular Gyrus	brain
10	chr16:46888400-46891200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr16:46888400-46891200	Weak transcription	Fetal Muscle Leg	muscle
12	chr16:46888400-46891200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr16:46888400-46896600	Weak transcription	Pancreas	Pancrea
14	chr16:46888400-46913400	Weak transcription	Esophagus	oesophagus
15	chr16:46888600-46891000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:46888600-46891000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:46888600-46891200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:46888600-46891200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr16:46888600-46891600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:46889200-46890600	Enhancers	Stomach Mucosa	stomach
21	chr16:46890000-46890400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr16:46890000-46890400	Enhancers	Sigmoid Colon	Sigmoid Colon

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