Variant report

Variant	rs4889505
Chromosome Location	chr16:30772040-30772041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30771474-30772185	K562	blood:	n/a	n/a
2	POLR2A	chr16:30771517-30774521	K562	blood:	n/a	n/a
3	POLR2A	chr16:30771502-30772060	GM12878	blood:	n/a	n/a
4	NRF1	chr16:30772000-30774019	SK-N-SH	brain:	n/a	chr16:30773575-30773589 chr16:30773575-30773586
5	POLR2A	chr16:30771611-30772140	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:30771462-30773995	HL-60	blood:	n/a	n/a
7	POLR2A	chr16:30771522-30772145	MCF-7	breast:	n/a	n/a
8	POLR2A	chr16:30771884-30774041	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr16:30770464-30772098	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:30771609-30772070	GM12892	blood:	n/a	n/a
11	ELF1	chr16:30771779-30772129	K562	blood:	n/a	chr16:30771983-30771996
12	POLR2A	chr16:30771658-30772288	U87	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30771826..30774840-chr16:30967351..30969175,3	K562	blood:
2	chr16:30749695..30756203-chr16:30770648..30776596,12	K562	blood:
3	chr16:30770928..30773513-chr16:30952878..30954380,2	K562	blood:
4	chr16:30676794..30679147-chr16:30771507..30774609,3	MCF-7	breast:
5	chr16:30708170..30712232-chr16:30770048..30773747,7	MCF-7	breast:
6	chr16:30749130..30756602-chr16:30770748..30777685,19	MCF-7	breast:
7	chr16:30770838..30772695-chr16:30960014..30962052,2	K562	blood:
8	chr16:30771138..30775135-chr16:30932116..30935546,5	K562	blood:
9	chr16:30712607..30714306-chr16:30771326..30773925,2	K562	blood:
10	chr16:30771064..30772842-chr16:30931594..30934541,3	MCF-7	breast:
11	chr16:30708426..30712348-chr16:30772033..30775384,7	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHKG2-1	chr16:30770176-30772490	NONHSAT141810

No data

Variant related genes	Relation type
RNF40	TF binding region
C16orf93	TF binding region
ENSG00000099364	Chromatin interaction
ENSG00000222287	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000260899	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000260852	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10782000	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11150594	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11150595	0.94[YRI][hapmap]
rs11640414	0.87[AFR][1000 genomes]
rs11648654	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12596375	1.00[AMR][1000 genomes]
rs12596394	1.00[AMR][1000 genomes]
rs12598056	1.00[AMR][1000 genomes]
rs12931844	1.00[AMR][1000 genomes]
rs12933849	1.00[AMR][1000 genomes]
rs1348039	1.00[MKK][hapmap]
rs1530201	1.00[MKK][hapmap]
rs1550477	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs2053426	1.00[AMR][1000 genomes]
rs2099754	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2099755	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919430	1.00[AMR][1000 genomes]
rs2919431	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919432	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919433	1.00[AMR][1000 genomes]
rs2972804	1.00[AMR][1000 genomes]
rs2972808	0.84[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap]
rs2972809	0.82[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap]
rs2972815	1.00[AMR][1000 genomes]
rs4617878	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889488	1.00[AMR][1000 genomes]
rs4889494	1.00[AMR][1000 genomes]
rs4889500	1.00[LWK][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889501	1.00[AMR][1000 genomes]
rs4889502	1.00[MKK][hapmap]
rs4889503	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889504	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889506	1.00[MKK][hapmap]
rs4889508	0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889509	0.94[YRI][hapmap]
rs4889510	1.00[AMR][1000 genomes]
rs4889528	1.00[AMR][1000 genomes]
rs55635617	1.00[AMR][1000 genomes]
rs56038936	1.00[AMR][1000 genomes]
rs56209507	1.00[AMR][1000 genomes]
rs57225118	1.00[AMR][1000 genomes]
rs57643871	1.00[AMR][1000 genomes]
rs57877247	1.00[AMR][1000 genomes]
rs6420450	1.00[MKK][hapmap]
rs6565203	1.00[AMR][1000 genomes]
rs6565204	1.00[AMR][1000 genomes]
rs6565205	1.00[AMR][1000 genomes]
rs6565208	1.00[AMR][1000 genomes]
rs6565209	1.00[AMR][1000 genomes]
rs6565210	1.00[AMR][1000 genomes]
rs7185136	1.00[LWK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7188077	1.00[AMR][1000 genomes]
rs7188927	1.00[MKK][hapmap]
rs7193412	1.00[AMR][1000 genomes]
rs7194763	1.00[AMR][1000 genomes]
rs7195583	1.00[LWK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7195612	0.84[ASW][hapmap];1.00[AMR][1000 genomes]
rs73524581	1.00[AMR][1000 genomes]
rs73524584	1.00[AMR][1000 genomes]
rs73536457	1.00[AMR][1000 genomes]
rs73536466	1.00[AMR][1000 genomes]
rs73536474	1.00[AMR][1000 genomes]
rs73536488	1.00[AMR][1000 genomes]
rs73536498	1.00[AMR][1000 genomes]
rs73536499	1.00[AMR][1000 genomes]
rs8045484	0.93[YRI][hapmap]
rs8045550	1.00[AMR][1000 genomes]
rs8045624	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs8046609	1.00[AMR][1000 genomes]
rs8047743	1.00[AMR][1000 genomes]
rs8048656	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8049589	1.00[AMR][1000 genomes]
rs8050578	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8058475	1.00[AMR][1000 genomes]
rs893924	1.00[MKK][hapmap]
rs893925	1.00[MKK][hapmap]
rs893926	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs893927	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs9921630	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs9934046	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941201	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941300	1.00[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][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	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
11	nsv9438	chr16:30770203-30799442	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh 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	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30760000-30772400	Weak transcription	Stomach Mucosa	stomach
2	chr16:30760200-30772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:30760400-30772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:30760400-30772200	Weak transcription	Fetal Heart	heart
5	chr16:30760400-30772200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr16:30760400-30772200	Weak transcription	Small Intestine	intestine
7	chr16:30760600-30772200	Weak transcription	Psoas Muscle	Psoas
8	chr16:30760600-30772600	Weak transcription	Right Atrium	heart
9	chr16:30761200-30772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr16:30765200-30772200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:30765800-30772200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:30766400-30772200	Weak transcription	Fetal Kidney	kidney
13	chr16:30766600-30772200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr16:30766800-30772200	Weak transcription	NH-A	brain
15	chr16:30768000-30772200	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:30768200-30772200	Weak transcription	Fetal Lung	lung
17	chr16:30768400-30772200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:30768800-30772200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:30768800-30772200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:30768800-30772200	Weak transcription	Left Ventricle	heart
21	chr16:30769000-30772200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr16:30769000-30772200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr16:30769000-30772200	Weak transcription	Thymus	Thymus
24	chr16:30769000-30772600	Weak transcription	Aorta	Aorta
25	chr16:30769200-30772200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr16:30769200-30772200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:30769200-30772200	Weak transcription	Primary T cells from cord blood	blood
28	chr16:30769200-30772200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:30769200-30772200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:30769400-30772200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr16:30769400-30772200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr16:30769400-30772200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:30769400-30772200	Weak transcription	Brain Substantia Nigra	brain
34	chr16:30769400-30772200	Weak transcription	Ovary	ovary
35	chr16:30769400-30772200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr16:30769400-30772200	Weak transcription	HSMMtube	muscle
37	chr16:30769400-30772400	Weak transcription	Adipose Nuclei	Adipose
38	chr16:30769400-30772400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr16:30769800-30772400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr16:30769800-30772400	Weak transcription	A549	lung
41	chr16:30770000-30772200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr16:30770200-30772200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr16:30770200-30772200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
44	chr16:30770200-30772400	Enhancers	Primary B cells from peripheral blood	blood
45	chr16:30770200-30773200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr16:30770600-30772200	Weak transcription	Fetal Intestine Large	intestine
47	chr16:30770600-30772400	Weak transcription	Gastric	stomach
48	chr16:30771000-30772200	Enhancers	Primary B cells from cord blood	blood
49	chr16:30771000-30772200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:30771000-30772200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links