Variant report

Variant	rs8053883
Chromosome Location	chr16:70542721-70542722
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	CTCF	chr16:70542720-70542870	GM06990	blood:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
2	CTCF	chr16:70542660-70542930	HEEpiC	esophagus:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
3	CTCF	chr16:70542700-70542850	HFF	foreskin:	n/a	chr16:70542830-70542846
4	RAD21	chr16:70542615-70543095	HCT-116	colon:	n/a	chr16:70542830-70542849
5	STAT3	chr16:70542597-70542824	MCF10A-Er-Src	breast:	n/a	n/a
6	RAD21	chr16:70542704-70542963	SK-N-SH_RA	brain:	n/a	chr16:70542830-70542849
7	CTCF	chr16:70542720-70542870	AG04449	skin:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
8	RAD21	chr16:70542591-70542943	HepG2	liver:	n/a	chr16:70542830-70542849
9	RAD21	chr16:70542615-70543035	MCF-7	breast:	n/a	chr16:70542830-70542849
10	CTCF	chr16:70542621-70543058	MCF-7	breast:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
11	CTCF	chr16:70542700-70542850	GM12864	blood:	n/a	chr16:70542830-70542846
12	CTCF	chr16:70542660-70542810	HFF-Myc	foreskin:	n/a	n/a
13	CTCF	chr16:70542580-70542730	HMEC	breast:	n/a	n/a
14	CTCF	chr16:70542620-70542770	HVMF	connective:	n/a	n/a
15	CTCF	chr16:70542679-70543006	K562	blood:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
16	RAD21	chr16:70542670-70543056	A549	lung:	n/a	chr16:70542830-70542849
17	SMC3	chr16:70542691-70543042	GM12878	blood:	n/a	n/a
18	CTCF	chr16:70542693-70542991	HUVEC	blood vessel:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
19	TBL1XR1	chr16:70542655-70542927	K562	blood:	n/a	n/a
20	CTCF	chr16:70542580-70542730	BJ	skin:	n/a	n/a
21	RAD21	chr16:70542629-70543132	HCT-116	colon:	n/a	chr16:70542830-70542849
22	CTCF	chr16:70542640-70542790	BE2_C	brain:	n/a	n/a
23	RAD21	chr16:70542660-70543038	Hela-S3	cervix:	n/a	chr16:70542830-70542849
24	CTCF	chr16:70542720-70542870	HCM	heart:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
25	CTCF	chr16:70542700-70542930	HVMF	connective:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
26	CTCF	chr16:70542700-70542850	HRE	kidney:	n/a	chr16:70542830-70542846
27	CTCF	chr16:70542700-70542970	GM12865	blood:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
28	ZNF143	chr16:70542693-70542986	GM12878	blood:	n/a	n/a
29	CTCF	chr16:70542646-70543038	GM12878	blood:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
30	RAD21	chr16:70542717-70542966	GM12878	blood:	n/a	chr16:70542830-70542849
31	CTCF	chr16:70542658-70542986	A549	lung:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
32	CTCF	chr16:70542700-70542850	HepG2	liver:	n/a	chr16:70542830-70542846
33	CTCF	chr16:70542720-70542870	HBMEC	blood vessel:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
34	CTCF	chr16:70542720-70542870	GM12865	blood:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
35	CTCF	chr16:70542720-70542870	SAEC	small airway:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
36	RAD21	chr16:70542655-70543061	GM12878	blood:	n/a	chr16:70542830-70542849
37	CTCF	chr16:70542720-70542870	HEK293	kidney:	n/a	chr16:70542830-70542846 chr16:70542831-70542852
38	CTCF	chr16:70542720-70542870	HCT-116	colon:	n/a	chr16:70542830-70542846 chr16:70542831-70542852

No.	Distal block	Cell Line	Cell type
1	chr16:70412934..70415272-chr16:70540814..70543390,2	MCF-7	breast:
2	chr16:70540803..70547043-chr16:70555255..70559706,8	MCF-7	breast:
3	chr16:70542244..70550034-chr16:70550058..70558887,15	MCF-7	breast:

Variant related genes	Relation type
COG4	TF binding region
ENSG00000189091	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11859870	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11860870	0.91[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs11861097	1.00[EUR][1000 genomes]
rs11861486	0.85[AMR][1000 genomes]
rs11863943	0.83[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes]
rs11864179	0.92[AMR][1000 genomes]
rs11864326	0.84[AMR][1000 genomes]
rs11865484	0.92[AMR][1000 genomes]
rs11865564	0.84[AMR][1000 genomes]
rs16970121	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs16970133	1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970141	0.91[ASW][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs16970147	0.91[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs16970149	0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970151	0.83[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970152	0.83[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970153	0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970159	0.83[ASW][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970165	0.83[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970169	0.83[ASW][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs16970331	1.00[EUR][1000 genomes]
rs16970335	1.00[EUR][1000 genomes]
rs16970609	0.91[ASW][hapmap];0.81[YRI][hapmap]
rs17878609	0.84[AMR][1000 genomes]
rs17879665	0.92[AMR][1000 genomes]
rs17880268	0.91[ASW][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes]
rs17881219	1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs17882471	1.00[MEX][hapmap]
rs35904382	0.85[AMR][1000 genomes]
rs4999488	0.84[AMR][1000 genomes]
rs55769835	0.92[AMR][1000 genomes]
rs55775924	0.92[AMR][1000 genomes]
rs55916527	0.92[AMR][1000 genomes]
rs55963712	1.00[EUR][1000 genomes]
rs56050266	0.85[AMR][1000 genomes]
rs56082018	0.92[AMR][1000 genomes]
rs56096542	1.00[EUR][1000 genomes]
rs56348821	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56836664	0.85[AMR][1000 genomes]
rs57150196	1.00[EUR][1000 genomes]
rs57492770	1.00[EUR][1000 genomes]
rs58047061	0.85[AMR][1000 genomes]
rs58434182	1.00[EUR][1000 genomes]
rs59260159	1.00[EUR][1000 genomes]
rs59552467	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60011151	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60045805	0.85[AMR][1000 genomes]
rs60387488	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60646112	0.92[AMR][1000 genomes]
rs61284127	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61319691	0.84[AMR][1000 genomes]
rs61369696	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61391917	1.00[EUR][1000 genomes]
rs6499312	0.85[AMR][1000 genomes]
rs6499314	0.91[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs7184248	1.00[EUR][1000 genomes]
rs7188864	0.85[AMR][1000 genomes]
rs7189535	1.00[EUR][1000 genomes]
rs7190536	0.92[AMR][1000 genomes]
rs7195086	0.83[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes]
rs7195104	0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7195567	0.91[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs7199043	1.00[EUR][1000 genomes]
rs7199145	1.00[MEX][hapmap]
rs7199346	0.91[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs7199655	0.85[AMR][1000 genomes]
rs7203548	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203761	1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203772	1.00[MEX][hapmap]
rs7205871	1.00[EUR][1000 genomes]
rs7205990	0.91[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs7206347	0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs74024196	1.00[EUR][1000 genomes]
rs74026026	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74026033	0.84[AMR][1000 genomes]
rs74026049	0.92[AMR][1000 genomes]
rs8049046	0.81[YRI][hapmap]
rs8049316	1.00[MEX][hapmap]
rs8050252	1.00[EUR][1000 genomes]
rs8053040	0.81[YRI][hapmap]
rs8054203	0.85[AMR][1000 genomes]
rs8055338	1.00[MEX][hapmap]
rs8056811	1.00[MEX][hapmap]
rs8058032	1.00[EUR][1000 genomes]
rs8058735	0.92[AMR][1000 genomes]
rs8062602	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70518000-70545800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:70528000-70553800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr16:70528800-70556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:70530600-70545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:70531000-70542800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr16:70531400-70543600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr16:70531600-70542800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr16:70532000-70542800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:70532000-70543000	Weak transcription	Colonic Mucosa	Colon
12	chr16:70532000-70543000	Weak transcription	Small Intestine	intestine
13	chr16:70532000-70545600	Weak transcription	A549	lung
14	chr16:70533400-70543000	Weak transcription	Gastric	stomach
15	chr16:70536600-70554000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:70536800-70546200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:70536800-70554000	Strong transcription	Fetal Stomach	stomach
18	chr16:70537000-70546400	Strong transcription	Fetal Intestine Small	intestine
19	chr16:70537200-70554000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:70537800-70542800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:70537800-70552600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr16:70537800-70553800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:70537800-70553800	Strong transcription	Liver	Liver
24	chr16:70538000-70543000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:70538600-70543000	Weak transcription	Lung	lung
26	chr16:70538800-70552200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr16:70539600-70552400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr16:70539600-70553800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:70539800-70542800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr16:70539800-70543200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr16:70539800-70552000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr16:70539800-70552600	Strong transcription	Primary T cells from cord blood	blood
33	chr16:70539800-70552600	Strong transcription	Fetal Intestine Large	intestine
34	chr16:70539800-70552600	Strong transcription	Fetal Muscle Leg	muscle
35	chr16:70539800-70553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:70539800-70553800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr16:70539800-70553800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:70539800-70553800	Strong transcription	Placenta	Placenta
39	chr16:70540000-70546400	Strong transcription	Pancreas	Pancrea
40	chr16:70540000-70552400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr16:70540000-70553000	Strong transcription	Thymus	Thymus
42	chr16:70540200-70551000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:70540200-70553800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr16:70540200-70554000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr16:70540400-70542800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr16:70540400-70544000	Strong transcription	NHLF	lung
47	chr16:70540400-70546000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr16:70540400-70546000	Strong transcription	Osteobl	bone
49	chr16:70540400-70552600	Strong transcription	Brain Germinal Matrix	brain
50	chr16:70540600-70542800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links