Variant report

Variant	rs4966706
Chromosome Location	chr16:46916727-46916728
allele	A/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	chr16:46916251-46918645	HepG2	liver:	n/a	n/a
2	TEAD4	chr16:46916143-46916877	HepG2	liver:	n/a	n/a
3	EP300	chr16:46916491-46916776	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:46916706-46916754	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYBL2	chr16:46916124-46918353	HepG2	liver:	n/a	n/a
6	MAX	chr16:46916479-46916747	HepG2	liver:	n/a	n/a
7	HNF4A	chr16:46916329-46916855	HepG2	liver:	n/a	chr16:46916636-46916648
8	RXRA	chr16:46916309-46916897	HepG2	liver:	n/a	n/a
9	FOSL2	chr16:46916258-46916873	HepG2	liver:	n/a	n/a
10	HDAC2	chr16:46916152-46916905	HepG2	liver:	n/a	chr16:46916638-46916646
11	JUND	chr16:46916292-46916884	HepG2	liver:	n/a	n/a
12	HEY1	chr16:46916133-46918947	HepG2	liver:	n/a	chr16:46918010-46918025 chr16:46918124-46918139 chr16:46918214-46918229 chr16:46918437-46918452
13	CEBPB	chr16:46916388-46916773	HepG2	liver:	n/a	n/a
14	JUND	chr16:46916376-46916758	HepG2	liver:	n/a	n/a
15	HNF4G	chr16:46916367-46916787	HepG2	liver:	n/a	chr16:46916636-46916648
16	HEY1	chr16:46916303-46918141	HepG2	liver:	n/a	chr16:46918010-46918025 chr16:46918124-46918139
17	FOXA1	chr16:46916318-46917044	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:46916727-46918498	MCF10A-Er-Src	breast:	n/a	n/a
19	NFIC	chr16:46916131-46918159	HepG2	liver:	n/a	n/a
20	EP300	chr16:46916155-46916937	HepG2	liver:	n/a	chr16:46916190-46916206
21	MBD4	chr16:46915922-46918097	HepG2	liver:	n/a	n/a
22	POLR2A	chr16:46916413-46918595	HepG2	liver:	n/a	n/a
23	CREB1	chr16:46916064-46919268	HepG2	liver:	n/a	n/a
24	FOSL2	chr16:46916245-46916898	HepG2	liver:	n/a	n/a
25	ATF3	chr16:46916480-46916776	HepG2	liver:	n/a	n/a
26	POLR2A	chr16:46916429-46918545	HepG2	liver:	n/a	n/a
27	NFIC	chr16:46916088-46918258	HepG2	liver:	n/a	n/a
28	ZEB1	chr16:46916172-46917353	HepG2	liver:	n/a	chr16:46916888-46916896
29	POLR2A	chr16:46916571-46917137	HepG2	liver:	n/a	n/a
30	HDAC2	chr16:46916015-46916850	HepG2	liver:	n/a	chr16:46916638-46916646 chr16:46916056-46916070
31	FOXA1	chr16:46916186-46916915	HepG2	liver:	n/a	n/a
32	RCOR1	chr16:46916225-46916779	K562	blood:	n/a	n/a
33	CEBPB	chr16:46916385-46916786	HepG2	liver:	n/a	n/a
34	FOXA2	chr16:46916268-46916888	HepG2	liver:	n/a	n/a
35	FOXA1	chr16:46916291-46916965	HepG2	liver:	n/a	n/a
36	EP300	chr16:46916273-46916855	HepG2	liver:	n/a	n/a
37	FOXA1	chr16:46916265-46916825	HepG2	liver:	n/a	n/a
38	POLR2A	chr16:46916503-46922808	HepG2	liver:	n/a	n/a
39	MBD4	chr16:46916089-46918202	HepG2	liver:	n/a	n/a
40	MXI1	chr16:46916323-46916821	HepG2	liver:	n/a	chr16:46916591-46916600
41	TBP	chr16:46916365-46917040	HepG2	liver:	n/a	n/a
42	MAX	chr16:46916487-46919276	NB4	blood:	n/a	chr16:46917871-46917880 chr16:46918074-46918084
43	GATA2	chr16:46916378-46916786	SH-SY5Y	brain:	n/a	n/a
44	POLR2A	chr16:46916226-46919725	H1-hESC	embryonic stem cell:	n/a	n/a
45	RFX5	chr16:46916314-46916801	HepG2	liver:	n/a	n/a
46	CEBPD	chr16:46916309-46916780	HepG2	liver:	n/a	n/a
47	ARID3A	chr16:46916320-46916793	HepG2	liver:	n/a	n/a
48	POLR2A	chr16:46916316-46918166	HepG2	liver:	n/a	n/a
49	REST	chr16:46916255-46917111	HepG2	liver:	n/a	n/a
50	MAZ	chr16:46916478-46916755	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:46916414..46917983-chr16:46954082..46956744,2	K562	blood:
2	chr16:46895641..46897768-chr16:46916063..46918079,2	K562	blood:
3	chr16:46916007..46917928-chr16:46919979..46921962,2	MCF-7	breast:
4	chr16:46898009..46901625-chr16:46916085..46918224,4	MCF-7	breast:

Variant related genes	Relation type
GPT2	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009391	1.00[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.92[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12930432	0.80[AFR][1000 genomes]
rs12934580	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1641122	1.00[ASN][1000 genomes]
rs1869006	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	1.00[ASN][1000 genomes]
rs35354454	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4246381	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.85[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.93[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.94[EUR][1000 genomes]
rs56042735	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.93[EUR][1000 genomes]
rs57127559	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	1.00[ASN][1000 genomes]
rs58074838	0.90[EUR][1000 genomes]
rs59708508	0.89[EUR][1000 genomes]
rs62057633	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	1.00[ASN][1000 genomes]
rs7186748	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7192574	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7196375	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.86[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs8053137	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	1.00[ASN][1000 genomes]
rs8058734	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	0.87[CEU][hapmap];0.97[YRI][hapmap];1.00[ASN][1000 genomes]
rs9328668	0.93[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[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	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
8	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
9	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
10	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1799095	chr16:46916670-46972671	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4966706	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46913600-46917000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr16:46914000-46917000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:46914000-46917000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:46914400-46917000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr16:46914400-46917200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr16:46914600-46917000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr16:46915600-46916800	Enhancers	Liver	Liver
8	chr16:46915800-46917400	Weak transcription	Right Atrium	heart
9	chr16:46916000-46916800	Enhancers	Pancreas	Pancrea
10	chr16:46916000-46917000	Enhancers	Brain Substantia Nigra	brain
11	chr16:46916000-46917000	Flanking Active TSS	HepG2	liver
12	chr16:46916000-46917400	Enhancers	Placenta	Placenta
13	chr16:46916200-46916800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr16:46916200-46916800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr16:46916200-46917000	Weak transcription	Adipose Nuclei	Adipose
16	chr16:46916200-46917200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr16:46916200-46917200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr16:46916200-46917200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr16:46916200-46917200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr16:46916200-46917200	Bivalent Enhancer	Fetal Kidney	kidney
21	chr16:46916200-46917600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr16:46916400-46917000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr16:46916400-46917000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr16:46916400-46917000	Enhancers	Brain Anterior Caudate	brain
25	chr16:46916400-46917200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:46916400-46917200	Enhancers	Brain Hippocampus Middle	brain
27	chr16:46916400-46917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:46916400-46917400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr16:46916400-46917400	Enhancers	Brain Angular Gyrus	brain
30	chr16:46916400-46917400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr16:46916400-46917400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr16:46916400-46917600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:46916600-46916800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr16:46916600-46916800	Enhancers	Gastric	stomach
35	chr16:46916600-46916800	Flanking Active TSS	K562	blood
36	chr16:46916600-46917000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr16:46916600-46917000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr16:46916600-46917000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
39	chr16:46916600-46917200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
40	chr16:46916600-46917400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:46916600-46917400	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr16:46916600-46917400	Enhancers	Esophagus	oesophagus
43	chr16:46916600-46917400	Enhancers	Stomach Mucosa	stomach

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