Variant report

Variant	rs4889661
Chromosome Location	chr16:31479200-31479201
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	POLR2A	chr16:31479114-31479215	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31479039-31479302	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:31478212-31479236	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:31478132-31479927	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TGFB1I1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11150624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1135265	0.82[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11643752	0.82[ASW][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11646054	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11646911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12920273	0.80[ASN][1000 genomes]
rs12923122	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12930621	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3116150	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs35884660	0.81[ASN][1000 genomes]
rs4243237	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4313820	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4482295	0.82[ASW][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs4597343	0.81[ASN][1000 genomes]
rs4889549	0.82[JPT][hapmap]
rs4889664	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4889666	0.81[ASN][1000 genomes]
rs7201796	0.81[ASN][1000 genomes]
rs7206531	0.81[ASN][1000 genomes]
rs8048218	0.82[ASW][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs8050563	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8050712	0.81[ASN][1000 genomes]

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	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4889661	FBXL19	cis	cerebellum	SCAN
rs4889661	FUS	cis	cerebellum	SCAN
rs4889661	NCRNA00095	cis	lymphoblastoid	seeQTL
rs4889661	TGFB1I1	cis	cerebellum	SCAN
rs4889661	ZNF646	cis	cerebellum	SCAN

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31471000-31482600	Weak transcription	Small Intestine	intestine
2	chr16:31471800-31483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:31472000-31480400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:31472000-31481800	Weak transcription	NHDF-Ad	bronchial
5	chr16:31472000-31482000	Weak transcription	Fetal Heart	heart
6	chr16:31472000-31482400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:31472000-31482400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr16:31472000-31482600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:31472000-31482600	Weak transcription	Stomach Mucosa	stomach
10	chr16:31472600-31482600	Weak transcription	Fetal Brain Male	brain
11	chr16:31472600-31483000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr16:31472800-31482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr16:31472800-31482400	Weak transcription	Hela-S3	cervix
14	chr16:31472800-31482400	Weak transcription	HMEC	breast
15	chr16:31472800-31482400	Weak transcription	HSMM	muscle
16	chr16:31473200-31479200	Strong transcription	Fetal Brain Female	brain
17	chr16:31473200-31479400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr16:31473600-31479400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:31475200-31482600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:31475200-31482600	Weak transcription	Fetal Kidney	kidney
21	chr16:31475400-31482000	Weak transcription	Colon Smooth Muscle	Colon
22	chr16:31475400-31482200	Weak transcription	Fetal Lung	lung
23	chr16:31475600-31479200	Strong transcription	Liver	Liver
24	chr16:31475800-31482400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:31476200-31482800	Weak transcription	Psoas Muscle	Psoas
26	chr16:31476400-31481400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr16:31476600-31482400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:31476600-31482400	Weak transcription	Primary T cells from cord blood	blood
29	chr16:31476800-31482600	Weak transcription	Brain Angular Gyrus	brain
30	chr16:31477000-31480000	Enhancers	Primary hematopoietic stem cells	blood
31	chr16:31477200-31482400	Weak transcription	HUVEC	blood vessel
32	chr16:31477400-31481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:31477400-31482400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr16:31477400-31482400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr16:31477400-31482400	Weak transcription	HSMMtube	muscle
36	chr16:31477600-31479200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr16:31477600-31482400	Weak transcription	HepG2	liver
38	chr16:31477600-31482600	Weak transcription	NHEK	skin
39	chr16:31477800-31479200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr16:31477800-31479200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr16:31477800-31480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:31477800-31480400	Enhancers	Dnd41	blood
43	chr16:31477800-31482400	Weak transcription	Fetal Intestine Large	intestine
44	chr16:31477800-31483600	Weak transcription	Brain Substantia Nigra	brain
45	chr16:31478000-31479200	Enhancers	Primary B cells from cord blood	blood
46	chr16:31478000-31479600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr16:31478200-31482200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:31478400-31479200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr16:31478400-31480000	Enhancers	Fetal Thymus	thymus
50	chr16:31478400-31482400	Weak transcription	Left Ventricle	heart

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