Variant report

Variant	rs8063455
Chromosome Location	chr16:71599977-71599978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:71598355-71600309	GM12878	blood:	n/a	n/a
2	RUNX3	chr16:71599950-71600601	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr16:71598258-71599981	MCF-7	breast:	n/a	n/a
4	IKZF1	chr16:71599282-71600534	GM12878	blood:	n/a	n/a
5	MEF2A	chr16:71599773-71600381	GM12878	blood:	n/a	n/a
6	FOXM1	chr16:71599909-71600490	GM12878	blood:	n/a	n/a
7	MXI1	chr16:71598368-71600237	GM12878	blood:	n/a	n/a
8	TEAD4	chr16:71598528-71599984	HepG2	liver:	n/a	n/a
9	CUX1	chr16:71599404-71600206	GM12878	blood:	n/a	n/a
10	EP300	chr16:71598507-71600358	GM12878	blood:	n/a	chr16:71598814-71598830 chr16:71598682-71598696
11	EBF1	chr16:71599522-71600330	GM12878	blood:	n/a	n/a
12	NFIC	chr16:71599147-71600569	GM12878	blood:	n/a	n/a
13	JUN	chr16:71599789-71600139	K562	blood:	n/a	n/a
14	PML	chr16:71598526-71600513	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:71598377-71600186	GM12891	blood:	n/a	n/a
16	STAT5A	chr16:71599170-71599980	GM12878	blood:	n/a	n/a
17	BCL11A	chr16:71599970-71600406	GM12878	blood:	n/a	n/a
18	CHD2	chr16:71599962-71600288	GM12878	blood:	n/a	n/a
19	MTA3	chr16:71598263-71600521	GM12878	blood:	n/a	n/a
20	SPI1	chr16:71599847-71600545	GM12878	blood:	n/a	n/a
21	RCOR1	chr16:71599833-71600603	GM12878	blood:	n/a	n/a
22	FOXA1	chr16:71599348-71600279	HepG2	liver:	n/a	n/a
23	CHD1	chr16:71599263-71600514	GM12878	blood:	n/a	n/a
24	FOXA1	chr16:71599320-71600259	HepG2	liver:	n/a	n/a
25	SMC3	chr16:71598622-71600217	GM12878	blood:	n/a	n/a
26	POLR2A	chr16:71599319-71599982	HepG2	liver:	n/a	n/a
27	MEF2A	chr16:71599900-71600482	GM12878	blood:	n/a	n/a
28	EP300	chr16:71598858-71600073	K562	blood:	n/a	n/a
29	FOXA1	chr16:71599387-71600325	HepG2	liver:	n/a	n/a
30	MYBL2	chr16:71598635-71600096	HepG2	liver:	n/a	n/a
31	GATA1	chr16:71598028-71600536	PBDE	blood:	n/a	n/a
32	ZNF384	chr16:71598654-71599983	K562	blood:	n/a	n/a
33	CTCF	chr16:71598065-71600034	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71597451..71600395-chr16:71660172..71663639,3	MCF-7	breast:
2	chr16:71516991..71518687-chr16:71598041..71600179,2	K562	blood:
3	chr16:71598139..71600865-chr16:71657563..71661455,3	MCF-7	breast:
4	chr16:71596888..71600063-chr16:71602973..71605498,3	MCF-7	breast:
5	chr16:71598954..71602131-chr16:71602948..71606674,3	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST4-2	chr16:71599954-71600104	ENSG00000260886.1
2	lnc-CHST4-2	chr16:71599954-71600104	NONHSAT143490
3	lnc-CHST4-2	chr16:71599954-71600104	NONHSAT143491
4	lnc-CHST4-2	chr16:71599954-71600104	NONHSAT143494

No data

Variant related genes	Relation type
RNU6-1061P	TF binding region
ZNF19	TF binding region
ENSG00000260593	Chromatin interaction
ENSG00000157429	Chromatin interaction
ENSG00000198650	Chromatin interaction
ENSG00000140832	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10500562	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12149264	0.90[CEU][hapmap]
rs12444890	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12446333	0.91[CEU][hapmap]
rs12447033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12919417	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12922775	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12923781	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12924650	0.91[CEU][hapmap];0.89[LWK][hapmap]
rs12927006	0.91[CEU][hapmap]
rs12927456	0.91[CEU][hapmap]
rs12927768	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12931191	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12935422	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17282500	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17345863	0.89[CEU][hapmap]
rs17347255	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17354693	0.91[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes]
rs17355804	0.91[CEU][hapmap];0.94[LWK][hapmap]
rs17356206	0.86[CEU][hapmap]
rs17356316	0.91[CEU][hapmap]
rs34181942	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34381861	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34753286	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35538253	0.89[AFR][1000 genomes]
rs71403859	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7203606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8051974	0.91[CEU][hapmap];1.00[GIH][hapmap]
rs8053720	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs8064179	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8063455	TK2	cis	parietal	SCAN
rs8063455	CTRL	cis	cerebellum	SCAN
rs8063455	NRN1L	cis	parietal	SCAN
rs8063455	RP11-432I5.1	cis	Thyroid	GTEx
rs8063455	ATP6V0D1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71598000-71600200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr16:71598200-71600000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr16:71598400-71600000	Active TSS	Osteobl	bone
4	chr16:71598400-71600400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr16:71599200-71600000	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr16:71599200-71600000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:71599200-71600400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr16:71599400-71600000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr16:71599400-71600000	Enhancers	Stomach Mucosa	stomach
10	chr16:71599400-71600000	Flanking Active TSS	HepG2	liver
11	chr16:71599400-71601800	Weak transcription	Esophagus	oesophagus
12	chr16:71599600-71600000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr16:71599600-71600000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr16:71599600-71600000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr16:71599600-71600000	Enhancers	Colon Smooth Muscle	Colon
16	chr16:71599600-71600000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr16:71599600-71600000	Flanking Active TSS	A549	lung
18	chr16:71599600-71600000	Flanking Active TSS	K562	blood
19	chr16:71599600-71600200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr16:71599600-71600600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr16:71599600-71600600	Flanking Active TSS	GM12878-XiMat	blood
22	chr16:71599600-71600800	Enhancers	Liver	Liver
23	chr16:71599600-71602000	Weak transcription	Right Atrium	heart
24	chr16:71599600-71605600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr16:71599600-71607800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr16:71599800-71600000	Enhancers	Primary T cells from cord blood	blood
27	chr16:71599800-71600000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr16:71599800-71600000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:71599800-71600000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr16:71599800-71600000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:71599800-71600000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr16:71599800-71600000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:71599800-71600000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:71599800-71600000	Enhancers	Duodenum Mucosa	Duodenum
35	chr16:71599800-71600000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr16:71599800-71600200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr16:71599800-71600200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr16:71599800-71600200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr16:71599800-71600200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr16:71599800-71600200	Enhancers	Small Intestine	intestine
41	chr16:71599800-71600200	Enhancers	Dnd41	blood
42	chr16:71599800-71600400	Weak transcription	Colonic Mucosa	Colon
43	chr16:71599800-71600600	Enhancers	Fetal Intestine Large	intestine
44	chr16:71599800-71600600	Enhancers	Fetal Intestine Small	intestine
45	chr16:71599800-71600600	Enhancers	Fetal Lung	lung
46	chr16:71599800-71601800	Weak transcription	Lung	lung
47	chr16:71599800-71602400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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