Variant report

Variant	rs41277712
Chromosome Location	chr15:52483641-52483642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52483608-52483660	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr15:52483576-52483730	K562	blood:	n/a	n/a
3	CTCF	chr15:52483560-52483710	A549	lung:	n/a	n/a
4	CTCF	chr15:52483637-52483718	MCF-7	breast:	n/a	n/a
5	CTCF	chr15:52483619-52483743	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr15:52483485-52483727	K562	blood:	n/a	n/a
7	POLR2A	chr15:52483435-52484150	MCF-7	breast:	n/a	n/a
8	POLR2A	chr15:52483462-52483811	ECC-1	luminal epithelium:	n/a	n/a
9	TAL1	chr15:52483564-52483770	K562	blood:	n/a	n/a
10	MYC	chr15:52483586-52483646	MCF-7	breast:	n/a	n/a
11	CTCF	chr15:52483523-52483759	K562	blood:	n/a	n/a
12	E2F6	chr15:52483448-52483674	K562	blood:	n/a	n/a
13	CTCF	chr15:52483540-52483690	HRPEpiC	eye:	n/a	n/a
14	MYC	chr15:52483554-52483646	K562	blood:	n/a	n/a
15	MAX	chr15:52483499-52483687	K562	blood:	n/a	n/a
16	CTCF	chr15:52483594-52483742	K562	blood:	n/a	n/a
17	CTCF	chr15:52483553-52483795	Medullo	brain:	n/a	n/a
18	POLR2A	chr15:52483637-52483647	HepG2	liver:	n/a	n/a
19	MAX	chr15:52483377-52483743	K562	blood:	n/a	n/a
20	CTCF	chr15:52483540-52483690	NHEK	skin:	n/a	n/a
21	CTCF	chr15:52483636-52483691	A549	lung:	n/a	n/a
22	CTCF	chr15:52483600-52483750	WERI-Rb-1	eye:	n/a	n/a
23	CTCF	chr15:52483560-52483710	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr15:52483620-52483770	SAEC	small airway:	n/a	n/a
25	CTCF	chr15:52483616-52483711	NHEK	skin:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
2	chr15:52472278..52474319-chr15:52482944..52484455,2	K562	blood:

No data

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16964751	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16964760	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16964764	0.87[AMR][1000 genomes]
rs17540171	1.00[AFR][1000 genomes]
rs17540546	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17540734	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17612637	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17612796	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2231289	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2414134	0.85[EUR][1000 genomes]
rs35581121	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41277704	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41277706	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776006	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776019	0.82[AMR][1000 genomes]
rs62016465	0.87[AMR][1000 genomes]
rs62016466	0.87[AMR][1000 genomes]
rs6493536	0.97[EUR][1000 genomes]
rs6493537	0.85[EUR][1000 genomes]
rs7168334	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177057	0.87[EUR][1000 genomes]
rs7181736	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73402856	0.82[EUR][1000 genomes]
rs73402857	0.90[EUR][1000 genomes]
rs74015635	0.80[EUR][1000 genomes]
rs8024846	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8024892	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473000-52483800	Weak transcription	A549	lung
2	chr15:52473000-52489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:52473200-52483800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:52473400-52485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:52473400-52496400	Weak transcription	Brain Anterior Caudate	brain
7	chr15:52473400-52496400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:52473400-52496600	Weak transcription	Spleen	Spleen
9	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
10	chr15:52474600-52488400	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:52476800-52484200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
15	chr15:52477800-52488000	Weak transcription	Gastric	stomach
16	chr15:52477800-52494800	Weak transcription	Fetal Intestine Large	intestine
17	chr15:52478000-52496200	Weak transcription	Liver	Liver
18	chr15:52478600-52488400	Weak transcription	Aorta	Aorta
19	chr15:52479600-52487400	Weak transcription	HepG2	liver
20	chr15:52479600-52495400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:52479600-52496400	Weak transcription	Esophagus	oesophagus
22	chr15:52479800-52485600	Weak transcription	Ovary	ovary
23	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
24	chr15:52481400-52485600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:52481600-52496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:52482000-52485600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:52482600-52496200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:52483400-52483800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:52483400-52483800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:52483400-52484000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr15:52483400-52484200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:52483400-52484200	Strong transcription	Fetal Intestine Small	intestine
33	chr15:52483400-52492400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:52483600-52483800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr15:52483600-52483800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:52483600-52483800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:52483600-52483800	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:52483600-52483800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:52483600-52484200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr15:52483600-52484200	Enhancers	Lung	lung
41	chr15:52483600-52484200	Strong transcription	Pancreas	Pancrea
42	chr15:52483600-52484400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:52483600-52484400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:52483600-52484800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52483600-52485600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:52483600-52485800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:52483600-52485800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:52483600-52488400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:52483600-52489200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:52483600-52496400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links