Variant report

Variant	rs11915720
Chromosome Location	chr3:156872705-156872706
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156872488-156872771	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:156868992-156873002	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:156872271-156872856	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:156872405-156872714	GM12878	blood:	n/a	n/a
5	CTCF	chr3:156872560-156872710	HAc	cerebellar:	n/a	n/a
6	POLR2A	chr3:156862893-156872946	A549	lung:	n/a	n/a
7	TBL1XR1	chr3:156872538-156872992	K562	blood:	n/a	n/a
8	POLR2A	chr3:156871943-156873244	Hela-S3	cervix:	n/a	n/a
9	EP300	chr3:156872637-156872877	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:156872234-156872987	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:156872516-156873496	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:156872184-156873097	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:156861007-156879269	K562	blood:	n/a	n/a
14	POLR2A	chr3:156863231-156878853	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:156872291-156872737	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:156868856-156872754	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:156872654-156872731	K562	blood:	n/a	n/a
18	POLR2A	chr3:156868728-156873222	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:156872238-156873494	Hela-S3	cervix:	n/a	n/a
20	GATA1	chr3:156872506-156873203	PBDE	blood:	n/a	chr3:156872507-156872518 chr3:156872888-156872905
21	CHD1	chr3:156868741-156879284	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:156863168-156879174	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr3:156872560-156872710	HMEC	breast:	n/a	n/a
24	CTCF	chr3:156872560-156872710	HPAF	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:156543622..156545874-chr3:156870977..156873628,2	MCF-7	breast:
2	chr3:156267016..156271448-chr3:156870182..156873447,4	K562	blood:
3	chr16:89939397..89940154-chr3:156872339..156872961,2	HCT-116	colon:
4	chr3:156267109..156271448-chr3:156870440..156873447,4	K562	blood:

No data

Variant related genes	Relation type
CCNL1	TF binding region
ENSG00000114850	Chromatin interaction
ENSG00000141002	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10513505	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11914788	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11917729	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16827306	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16827355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16827378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16827392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2047646	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2049241	1.00[EUR][1000 genomes]
rs2321741	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35965122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56810791	1.00[EUR][1000 genomes]
rs56844899	1.00[EUR][1000 genomes]
rs57016273	0.87[AFR][1000 genomes]
rs57897344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57942815	1.00[EUR][1000 genomes]
rs58794040	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59876369	1.00[EUR][1000 genomes]
rs60294797	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61173790	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762249	1.00[EUR][1000 genomes]
rs6764944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769050	0.94[AFR][1000 genomes]
rs6770855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6771465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785398	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6796862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6798526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6798588	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6798689	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6810035	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6810106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73873607	1.00[AMR][1000 genomes]
rs73873609	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73873615	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73873616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73873625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73878005	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7618940	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7619015	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7623711	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625819	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7630448	1.00[EUR][1000 genomes]
rs7635880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645454	1.00[EUR][1000 genomes]
rs7649998	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9756073	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr3:156855400-156877000	Weak transcription	Gastric	stomach
4	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:156858400-156876400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:156859400-156876200	Strong transcription	Placenta	Placenta
7	chr3:156860000-156872800	Strong transcription	HSMM	muscle
8	chr3:156860000-156874000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:156861200-156873000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:156861600-156873800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:156861800-156875600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:156863200-156876800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:156864000-156875600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:156864200-156872800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr3:156864800-156874600	Strong transcription	Fetal Thymus	thymus
16	chr3:156865400-156873600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:156865800-156874200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:156866200-156877000	Weak transcription	Esophagus	oesophagus
19	chr3:156866400-156874600	Weak transcription	Pancreas	Pancrea
20	chr3:156866400-156877000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:156867200-156875600	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:156867800-156874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:156869000-156874400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:156869000-156874600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:156869800-156874600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:156869800-156874600	Weak transcription	Spleen	Spleen
27	chr3:156869800-156876600	Weak transcription	Lung	lung
28	chr3:156870000-156874600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:156870400-156874600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:156870800-156874000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:156870800-156874400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:156870800-156875600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:156870800-156877000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr3:156871000-156877000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156871000-156877000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
36	chr3:156871400-156873200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:156871400-156874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:156871400-156874600	Weak transcription	Left Ventricle	heart
39	chr3:156871400-156875600	Genic enhancers	Fetal Lung	lung
40	chr3:156871400-156877000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:156871600-156873000	Genic enhancers	Brain Hippocampus Middle	brain
42	chr3:156871600-156873400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:156871600-156874400	Enhancers	Fetal Intestine Small	intestine
44	chr3:156871600-156875200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:156871600-156875400	Enhancers	Fetal Heart	heart
46	chr3:156871600-156876400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
47	chr3:156871600-156876800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
48	chr3:156871600-156877200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:156871600-156877200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr3:156871800-156873200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links