Variant report

Variant	rs9935222
Chromosome Location	chr16:31523926-31523927
allele	A/C
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	USF2	chr16:31523896-31523991	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31516846..31519269-chr16:31522678..31524630,2	MCF-7	breast:
2	chr16:31463366..31472153-chr16:31517209..31524290,14	MCF-7	breast:
3	chr16:31486171..31487950-chr16:31523746..31526284,2	K562	blood:

Variant related genes	Relation type
C16orf58	TF binding region
ENSG00000261474	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000260267	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11150626	0.92[JPT][hapmap]
rs1123498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12927208	0.93[ASN][1000 genomes]
rs13143	0.92[JPT][hapmap]
rs13337037	1.00[JPT][hapmap]
rs28692853	0.86[ASN][1000 genomes]
rs28813115	0.93[ASN][1000 genomes]
rs34497199	0.93[ASN][1000 genomes]
rs34742827	0.93[ASN][1000 genomes]
rs35856922	0.93[ASN][1000 genomes]
rs3934739	1.00[JPT][hapmap]
rs4468642	0.94[ASN][1000 genomes]
rs4519345	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4550470	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587995	0.94[ASN][1000 genomes]
rs4889548	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs4889673	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[ASN][1000 genomes]
rs6565236	1.00[JPT][hapmap]
rs6565241	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6565242	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67464975	0.93[ASN][1000 genomes]
rs7199801	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8046452	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8049216	0.93[ASN][1000 genomes]
rs8050390	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8057207	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8057401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9934336	1.00[JPT][hapmap]

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	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
8	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
9	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
10	nsv1060240	chr16:31495873-31581450	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	esv1823209	chr16:31521276-31580272	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9935222	AC026471.6	cis	lung	GTEx
rs9935222	MVP	cis	cerebellum	SCAN
rs9935222	SLC5A2	cis	lung	GTEx
rs9935222	AHSP	cis	parietal	SCAN
rs9935222	DCTPP1	cis	cerebellum	SCAN
rs9935222	PRR14	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31520800-31524000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr16:31520800-31524200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr16:31520800-31524200	Weak transcription	HMEC	breast
4	chr16:31520800-31524600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:31521000-31524000	Weak transcription	Osteobl	bone
6	chr16:31521000-31524200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr16:31521000-31524200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:31521200-31524200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:31521200-31524200	Weak transcription	Fetal Muscle Leg	muscle
10	chr16:31521400-31524000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr16:31521400-31524200	Weak transcription	NHEK	skin
12	chr16:31521400-31524400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:31521400-31525400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:31523600-31524400	ZNF genes & repeats	HSMM	muscle
15	chr16:31523600-31525600	Enhancers	HSMMtube	muscle
16	chr16:31523800-31524000	Enhancers	Psoas Muscle	Psoas
17	chr16:31523800-31524000	ZNF genes & repeats	K562	blood
18	chr16:31523800-31524200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr16:31523800-31524600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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