Variant report

Variant	rs60882887
Chromosome Location	chr11:47475675-47475676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr11:47475533-47476238	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr11:47475534-47476235	HCT-116	colon:	n/a	n/a
3	BCLAF1	chr11:47475663-47476178	GM12878	blood:	n/a	n/a
4	RAD21	chr11:47475629-47476105	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr11:47475550-47476566	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr11:47475660-47476162	ECC-1	luminal epithelium:	n/a	n/a
7	FOXA1	chr11:47475667-47476069	HepG2	liver:	n/a	n/a
8	RAD21	chr11:47475663-47476173	MCF-7	breast:	n/a	n/a
9	CBX3	chr11:47475638-47476179	K562	blood:	n/a	n/a
10	POLR2A	chr11:47475661-47475714	HepG2	liver:	n/a	n/a
11	CTCF	chr11:47475651-47476137	K562	blood:	n/a	n/a
12	CTCF	chr11:47475590-47476201	HCT-116	colon:	n/a	n/a
13	CTCF	chr11:47475672-47475675	GM13977	blood:	n/a	n/a
14	RAD21	chr11:47475664-47476158	A549	lung:	n/a	n/a
15	RAD21	chr11:47475607-47476230	MCF-7	breast:	n/a	n/a
16	CTCF	chr11:47475552-47476268	A549	lung:	n/a	n/a
17	POLR2A	chr11:47475527-47476007	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr11:47475632-47476071	MCF-7	breast:	n/a	n/a
19	RAD21	chr11:47475635-47476125	A549	lung:	n/a	n/a
20	TEAD4	chr11:47475664-47476166	HepG2	liver:	n/a	n/a
21	RAD21	chr11:47475638-47476178	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47394123..47395677-chr11:47474242..47477201,2	MCF-7	breast:
2	chr11:47395505..47396265-chr11:47475219..47475939,2	MCF-7	breast:
3	chr11:47376407..47377483-chr11:47475495..47476359,4	K562	blood:
4	chr11:47469326..47471997-chr11:47473720..47476376,2	MCF-7	breast:
5	chr11:47395073..47396141-chr11:47475486..47476579,4	MCF-7	breast:
6	chr11:47446223..47447873-chr11:47474244..47476501,2	MCF-7	breast:
7	chr11:47475117..47477912-chr11:47481556..47483873,3	K562	blood:

No data

Variant related genes	Relation type
RAPSN	TF binding region
ENSG00000165916	Chromatin interaction
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1044269	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10742805	0.84[ASN][1000 genomes]
rs10742806	0.83[ASN][1000 genomes]
rs10769267	0.83[ASN][1000 genomes]
rs11819955	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11820650	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11821273	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11821860	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11821917	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11822402	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11823490	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11824864	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11824971	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11824990	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11827106	0.85[ASN][1000 genomes]
rs11828339	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12282783	0.82[ASN][1000 genomes]
rs12419342	0.83[ASN][1000 genomes]
rs17198158	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17790804	0.95[ASN][1000 genomes]
rs2242511	0.92[ASN][1000 genomes]
rs34312154	0.80[EUR][1000 genomes]
rs3740684	0.82[ASN][1000 genomes]
rs3740685	0.83[ASN][1000 genomes]
rs3781628	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3824867	0.83[ASN][1000 genomes]
rs3847503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4237544	0.84[ASN][1000 genomes]
rs4282946	0.84[ASN][1000 genomes]
rs4384349	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752783	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752836	0.83[ASN][1000 genomes]
rs4752837	0.83[ASN][1000 genomes]
rs4752839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752843	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752992	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56756748	0.84[ASN][1000 genomes]
rs59631865	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60380053	0.84[ASN][1000 genomes]
rs60929305	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61000762	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7101772	0.82[ASN][1000 genomes]
rs7104366	0.82[ASN][1000 genomes]
rs7105122	0.82[ASN][1000 genomes]
rs7105907	0.82[ASN][1000 genomes]
rs7106142	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7107853	0.83[ASN][1000 genomes]
rs7108143	0.82[ASN][1000 genomes]
rs7111873	0.84[ASN][1000 genomes]
rs7115371	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7117277	0.84[ASN][1000 genomes]
rs7119556	0.82[ASN][1000 genomes]
rs7130693	0.84[ASN][1000 genomes]
rs753812	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7948705	0.82[ASN][1000 genomes]
rs9666924	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9733983	0.86[AFR][1000 genomes]
rs9734013	0.84[ASN][1000 genomes]
rs9919526	0.84[ASN][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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
3	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47457400-47488400	Weak transcription	Gastric	stomach
6	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:47464000-47481000	Weak transcription	NHEK	skin
10	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
11	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
12	chr11:47468800-47482200	Weak transcription	HUVEC	blood vessel
13	chr11:47471000-47480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:47471000-47480800	Weak transcription	Left Ventricle	heart
15	chr11:47471000-47480800	Weak transcription	Pancreas	Pancrea
16	chr11:47471000-47486200	Weak transcription	Right Ventricle	heart
17	chr11:47471200-47482200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:47471200-47488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:47471400-47479600	Weak transcription	Placenta	Placenta
20	chr11:47471400-47480600	Weak transcription	A549	lung
21	chr11:47471400-47480800	Weak transcription	Lung	lung
22	chr11:47471400-47489200	Weak transcription	HepG2	liver
23	chr11:47471600-47480600	Weak transcription	HSMM	muscle
24	chr11:47471600-47480600	Weak transcription	HSMMtube	muscle
25	chr11:47471600-47480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:47471600-47486000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:47471800-47475800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:47471800-47476400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:47471800-47485600	Weak transcription	Spleen	Spleen
30	chr11:47472000-47485600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:47474000-47485800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:47474600-47480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:47475000-47480600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:47475200-47482600	Weak transcription	NH-A	brain
35	chr11:47475400-47476000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:47475400-47479800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:47475400-47480200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:47475600-47475800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:47475600-47475800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:47475600-47475800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr11:47475600-47475800	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr11:47475600-47476000	Enhancers	Liver	Liver
43	chr11:47475600-47476000	Enhancers	Brain Cingulate Gyrus	brain
44	chr11:47475600-47476000	Enhancers	Brain Hippocampus Middle	brain
45	chr11:47475600-47476000	Enhancers	Colon Smooth Muscle	Colon
46	chr11:47475600-47476000	Enhancers	Fetal Muscle Leg	muscle
47	chr11:47475600-47476200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr11:47475600-47476200	Enhancers	Brain Anterior Caudate	brain
49	chr11:47475600-47476200	Enhancers	Fetal Muscle Trunk	muscle
50	chr11:47475600-47476200	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links