Variant report

Variant	rs3934739
Chromosome Location	chr16:31513086-31513087
allele	C/T
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	FOXA1	chr16:31512887-31513380	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31512678-31514852	HepG2	liver:	n/a	n/a
3	FOXA2	chr16:31512999-31513300	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:31513039-31517710	K562	blood:	n/a	n/a
5	HNF4A	chr16:31512864-31513328	HepG2	liver:	n/a	chr16:31513105-31513120 chr16:31513105-31513120 chr16:31513105-31513120 chr16:31513104-31513119
6	RCOR1	chr16:31513070-31513226	HepG2	liver:	n/a	n/a
7	ARID3A	chr16:31512937-31513312	HepG2	liver:	n/a	n/a
8	FOXA1	chr16:31512892-31513358	HepG2	liver:	n/a	n/a
9	HNF4G	chr16:31512863-31513254	HepG2	liver:	n/a	chr16:31513105-31513120 chr16:31513105-31513120 chr16:31513105-31513120
10	RCOR1	chr16:31513028-31513209	K562	blood:	n/a	n/a
11	CEBPB	chr16:31512917-31513087	HepG2	liver:	n/a	n/a
12	HNF4A	chr16:31512842-31513332	HepG2	liver:	n/a	chr16:31513105-31513120 chr16:31513105-31513120 chr16:31513105-31513120 chr16:31513104-31513119
13	CEBPB	chr16:31512915-31513220	HepG2	liver:	n/a	n/a
14	SMC3	chr16:31512979-31513193	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31508912..31513251-chr16:31517622..31519683,6	MCF-7	breast:
2	chr16:31498274..31499932-chr16:31512274..31514495,2	MCF-7	breast:
3	chr16:31503646..31506421-chr16:31512902..31514894,2	MCF-7	breast:
4	chr16:31512832..31514586-chr16:31721396..31723098,2	MCF-7	breast:

Variant related genes	Relation type
C16orf58	TF binding region
ENSG00000140675	Chromatin interaction
ENSG00000260740	Chromatin interaction
ENSG00000140688	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11150626	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11865835	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13143	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13337037	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34081766	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519345	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4889548	1.00[JPT][hapmap]
rs4889673	1.00[JPT][hapmap]
rs6565235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6565236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565242	1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7188278	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8057401	1.00[JPT][hapmap]
rs8062314	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926717	0.94[EUR][1000 genomes]
rs9934336	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9935222	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3934739	INO80E	cis	parietal	SCAN
rs3934739	SLC5A2	cis	lung	GTEx
rs3934739	PRR14	cis	cerebellum	SCAN
rs3934739	AHSP	cis	parietal	SCAN
rs3934739	FBXL19	cis	cerebellum	SCAN
rs3934739	AC026471.6	cis	lung	GTEx
rs3934739	TAOK2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31499800-31516200	Weak transcription	GM12878-XiMat	blood
2	chr16:31499800-31517200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:31499800-31517400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr16:31500400-31514200	Weak transcription	Fetal Heart	heart
5	chr16:31500400-31518000	Weak transcription	Small Intestine	intestine
6	chr16:31500600-31518200	Weak transcription	Stomach Mucosa	stomach
7	chr16:31501200-31513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr16:31501800-31518200	Weak transcription	Hela-S3	cervix
9	chr16:31502000-31518200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr16:31502600-31514600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr16:31503000-31513400	Strong transcription	Osteobl	bone
12	chr16:31504800-31513200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr16:31504800-31515200	Weak transcription	HUVEC	blood vessel
14	chr16:31505200-31518200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr16:31506800-31513400	Strong transcription	Primary hematopoietic stem cells	blood
16	chr16:31508200-31518200	Weak transcription	HMEC	breast
17	chr16:31508600-31517400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr16:31510000-31519000	Weak transcription	Aorta	Aorta
19	chr16:31510200-31518000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr16:31510200-31518400	Weak transcription	Fetal Kidney	kidney
21	chr16:31510600-31515200	Weak transcription	Psoas Muscle	Psoas
22	chr16:31511200-31513200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:31511200-31518600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr16:31511200-31518600	Weak transcription	Fetal Thymus	thymus
25	chr16:31511200-31518800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:31511400-31516200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr16:31511400-31518200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr16:31511600-31516400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr16:31511800-31514000	Weak transcription	HSMMtube	muscle
30	chr16:31511800-31514200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:31511800-31516200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr16:31511800-31516400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr16:31511800-31517400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr16:31511800-31517400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr16:31511800-31518200	Weak transcription	A549	lung
36	chr16:31511800-31518400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:31512000-31513400	Enhancers	Liver	Liver
38	chr16:31512000-31515200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:31512000-31515400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:31512000-31515600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr16:31512000-31516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:31512000-31516200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:31512000-31516600	Weak transcription	Primary B cells from cord blood	blood
44	chr16:31512000-31516800	Weak transcription	Brain Anterior Caudate	brain
45	chr16:31512000-31516800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:31512000-31516800	Weak transcription	Fetal Intestine Large	intestine
47	chr16:31512000-31516800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr16:31512000-31516800	Weak transcription	NHEK	skin
49	chr16:31512000-31517200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:31512000-31518000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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