Variant report

Variant	rs4889545
Chromosome Location	chr16:31521276-31521277
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	GATA1	chr16:31520419-31521500	K562	blood:	n/a	chr16:31520697-31520714 chr16:31521205-31521226 chr16:31520533-31520549 chr16:31521208-31521224 chr16:31520696-31520703
2	IRF1	chr16:31521133-31521394	K562	blood:	n/a	n/a
3	TAL1	chr16:31519148-31521406	K562	blood:	n/a	chr16:31520696-31520714
4	GATA1	chr16:31519552-31521465	PBDE	blood:	n/a	chr16:31520697-31520714 chr16:31521205-31521226 chr16:31520533-31520549 chr16:31521208-31521224 chr16:31520696-31520703
5	POLR2A	chr16:31518930-31521337	K562	blood:	n/a	n/a
6	MYC	chr16:31519062-31521295	K562	blood:	n/a	n/a
7	MAZ	chr16:31521137-31521337	K562	blood:	n/a	n/a
8	CBX3	chr16:31520885-31521376	K562	blood:	n/a	n/a
9	POLR2A	chr16:31520944-31521312	HepG2	liver:	n/a	n/a
10	CCNT2	chr16:31521228-31521446	K562	blood:	n/a	n/a
11	EP300	chr16:31519464-31521360	K562	blood:	n/a	chr16:31520458-31520472 chr16:31519751-31519758 chr16:31520196-31520210 chr16:31520186-31520200
12	ARID3A	chr16:31520511-31521392	K562	blood:	n/a	n/a
13	TEAD4	chr16:31520076-31521469	K562	blood:	n/a	n/a
14	POLR2A	chr16:31519496-31521433	K562	blood:	n/a	n/a
15	NR2F2	chr16:31519514-31521342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31494997..31499043-chr16:31517756..31521950,4	K562	blood:
2	chr16:31482449..31485901-chr16:31517810..31523430,5	MCF-7	breast:
3	chr16:31516310..31522725-chr16:31722480..31728998,9	MCF-7	breast:
4	chr16:30959582..30963121-chr16:31518179..31521498,3	K562	blood:
5	chr16:31468357..31473774-chr16:31516772..31522690,14	K562	blood:
6	chr16:31463366..31472153-chr16:31517209..31524290,14	MCF-7	breast:
7	chr16:31517989..31521434-chr16:31710261..31713968,8	MCF-7	breast:
8	chr16:31468899..31473390-chr16:31518411..31522821,12	MCF-7	breast:
9	chr16:31464355..31466816-chr16:31518466..31521334,2	K562	blood:
10	chr16:31468972..31472729-chr16:31517678..31523478,11	K562	blood:
11	chr16:31505926..31509513-chr16:31519166..31521852,3	K562	blood:
12	chr16:31518205..31521975-chr16:31709546..31713435,8	MCF-7	breast:
13	chr16:31519157..31521632-chr16:31883498..31885614,2	K562	blood:

Variant related genes	Relation type
C16orf58	TF binding region
ENSG00000185947	Chromatin interaction
ENSG00000261487	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000131797	Chromatin interaction
ENSG00000261474	Chromatin interaction
ENSG00000260568	Chromatin interaction
ENSG00000140675	Chromatin interaction
ENSG00000261731	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000140682	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000140688	Chromatin interaction

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

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

rs_ID	r²[population]
rs11150627	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11866003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13338939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13339026	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28509322	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813008	0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4296276	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4411513	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4499252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4503808	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889667	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889670	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889671	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889672	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56060924	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57204609	0.93[ASN][1000 genomes]
rs58618301	0.93[ASN][1000 genomes]
rs58729087	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59813627	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60075107	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61183892	0.93[ASN][1000 genomes]
rs62053184	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62053205	0.92[ASN][1000 genomes]
rs62053209	0.90[ASN][1000 genomes]
rs62053210	0.90[ASN][1000 genomes]
rs7196319	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7203199	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047112	0.82[EUR][1000 genomes]
rs8056084	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs8057393	0.92[ASN][1000 genomes]
rs9921592	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9921597	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9923241	0.92[ASN][1000 genomes]
rs9923480	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9929825	0.92[ASN][1000 genomes]
rs9937077	0.92[ASN][1000 genomes]
rs9937367	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889545	ERAF	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31518400-31521400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:31519000-31521400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr16:31520000-31521400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:31520600-31521400	Enhancers	Primary B cells from peripheral blood	blood
5	chr16:31520600-31521400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:31520600-31521400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr16:31520600-31521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr16:31520600-31521800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr16:31520600-31521800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:31520600-31521800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:31520600-31523000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr16:31520600-31523600	Weak transcription	Esophagus	oesophagus
13	chr16:31520800-31521400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr16:31520800-31521400	Enhancers	Primary T cells from cord blood	blood
15	chr16:31520800-31521400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr16:31520800-31521400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr16:31520800-31521400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr16:31520800-31521400	Enhancers	Adipose Nuclei	Adipose
19	chr16:31520800-31521400	Enhancers	Liver	Liver
20	chr16:31520800-31521400	Active TSS	Brain Angular Gyrus	brain
21	chr16:31520800-31521400	Enhancers	Brain Hippocampus Middle	brain
22	chr16:31520800-31521400	Enhancers	Colon Smooth Muscle	Colon
23	chr16:31520800-31521400	Enhancers	Duodenum Mucosa	Duodenum
24	chr16:31520800-31521400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr16:31520800-31521400	Enhancers	Fetal Lung	lung
26	chr16:31520800-31521400	Enhancers	Rectal Smooth Muscle	rectum
27	chr16:31520800-31521400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr16:31520800-31521400	Enhancers	Thymus	Thymus
29	chr16:31520800-31521400	Enhancers	GM12878-XiMat	blood
30	chr16:31520800-31521400	Enhancers	Hela-S3	cervix
31	chr16:31520800-31521400	Enhancers	HepG2	liver
32	chr16:31520800-31521400	Enhancers	HSMMtube	muscle
33	chr16:31520800-31521400	Enhancers	NHEK	skin
34	chr16:31520800-31521600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:31520800-31521600	Enhancers	Brain Anterior Caudate	brain
36	chr16:31520800-31521800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr16:31520800-31521800	Enhancers	Left Ventricle	heart
38	chr16:31520800-31521800	Enhancers	Pancreas	Pancrea
39	chr16:31520800-31522200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr16:31520800-31523600	Weak transcription	HSMM	muscle
41	chr16:31520800-31524000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr16:31520800-31524200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:31520800-31524200	Weak transcription	HMEC	breast
44	chr16:31520800-31524600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr16:31521000-31521400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr16:31521000-31521400	Enhancers	Primary hematopoietic stem cells	blood
47	chr16:31521000-31521400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:31521000-31521400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr16:31521000-31521600	Flanking Active TSS	K562	blood
50	chr16:31521000-31524000	Weak transcription	Osteobl	bone

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