Variant report

Variant	rs11633569
Chromosome Location	chr15:78296793-78296794
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	EP300	chr15:78296517-78297046	GM12878	blood:	n/a	n/a
2	REST	chr15:78296473-78296849	PFSK-1	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
3	REST	chr15:78296448-78296861	GM12878	blood:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
4	POLR2A	chr15:78296326-78297011	GM12878	blood:	n/a	n/a
5	WRNIP1	chr15:78296579-78296884	GM12878	blood:	n/a	n/a
6	RELA	chr15:78296667-78297052	GM19193	blood:	n/a	n/a
7	STAT1	chr15:78296770-78296946	GM12878	blood:	n/a	n/a
8	ZNF143	chr15:78296668-78296965	GM12878	blood:	n/a	chr15:78296752-78296770
9	PAX5	chr15:78296638-78296878	GM12878	blood:	n/a	n/a
10	MAX	chr15:78296598-78297230	GM12878	blood:	n/a	n/a
11	RELA	chr15:78296561-78297124	GM10847	blood:	n/a	n/a
12	REST	chr15:78296525-78296823	SK-N-SH	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
13	CREB1	chr15:78296587-78297090	GM12878	blood:	n/a	n/a
14	REST	chr15:78296470-78296891	U87	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
15	RELA	chr15:78296688-78297050	GM18526	blood:	n/a	n/a
16	BHLHE40	chr15:78296661-78297284	GM12878	blood:	n/a	n/a
17	RUNX3	chr15:78296551-78297086	GM12878	blood:	n/a	n/a
18	REST	chr15:78296489-78296835	H1-hESC	embryonic stem cell:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
19	POLR2A	chr15:78296541-78297037	GM12878	blood:	n/a	n/a
20	PML	chr15:78296737-78296888	GM12878	blood:	n/a	n/a
21	PAX5	chr15:78296473-78297051	GM12878	blood:	n/a	n/a
22	REST	chr15:78296472-78296889	U87	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
23	RELA	chr15:78296607-78297043	GM12892	blood:	n/a	n/a
24	SP1	chr15:78296716-78297022	GM12878	blood:	n/a	n/a
25	RELA	chr15:78296638-78297096	GM18951	blood:	n/a	n/a
26	USF2	chr15:78296726-78297040	GM12878	blood:	n/a	n/a
27	ZNF384	chr15:78296670-78297066	GM12878	blood:	n/a	n/a
28	REST	chr15:78296427-78296983	ECC-1	luminal epithelium:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
29	REST	chr15:78296463-78296881	PFSK-1	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
30	NFIC	chr15:78296695-78297090	GM12878	blood:	n/a	n/a
31	REST	chr15:78296446-78296888	MCF-7	breast:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
32	REST	chr15:78296586-78296810	SK-N-SH	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
33	RELA	chr15:78296638-78297094	GM18505	blood:	n/a	n/a
34	ATF2	chr15:78296576-78297071	GM12878	blood:	n/a	n/a
35	REST	chr15:78296457-78296831	H1-hESC	embryonic stem cell:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
36	REST	chr15:78296403-78296888	ECC-1	luminal epithelium:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
37	TBL1XR1	chr15:78296673-78297093	GM12878	blood:	n/a	n/a
38	STAT3	chr15:78296759-78297275	GM12878	blood:	n/a	chr15:78297029-78297037
39	EP300	chr15:78296650-78297216	GM12878	blood:	n/a	n/a
40	REST	chr15:78296515-78296862	SK-N-SH	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
41	RELA	chr15:78296644-78297368	GM12878	blood:	n/a	n/a
42	REST	chr15:78296391-78296876	MCF-7	breast:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
43	REST	chr15:78296523-78296882	PANC-1	pancreas:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
44	POLR2A	chr15:78296544-78296963	GM12892	blood:	n/a	n/a
45	REST	chr15:78296431-78296904	PFSK-1	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
46	POLR2A	chr15:78296655-78296834	GM12878	blood:	n/a	n/a
47	REST	chr15:78296485-78296813	PANC-1	pancreas:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
48	RELA	chr15:78296627-78297062	GM15510	blood:	n/a	n/a
49	MXI1	chr15:78296569-78297130	GM12878	blood:	n/a	n/a
50	CHD2	chr15:78296646-78297078	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1053506	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11633329	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854102	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12595595	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900731	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901492	1.00[ASN][1000 genomes]
rs12913206	1.00[ASN][1000 genomes]
rs12915731	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915847	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17477813	0.80[AFR][1000 genomes]
rs1837911	1.00[ASN][1000 genomes]
rs1837912	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867984	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4243073	0.84[AFR][1000 genomes]
rs4316722	1.00[ASN][1000 genomes]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886985	1.00[ASN][1000 genomes]
rs4886986	1.00[ASN][1000 genomes]
rs4886987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886993	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886997	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886998	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs4997420	0.82[AFR][1000 genomes]
rs61732053	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	1.00[ASN][1000 genomes]
rs7169381	0.81[AFR][1000 genomes]
rs7169882	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170452	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025423	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033216	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894295	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788640	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78283400-78305000	Weak transcription	K562	blood
2	chr15:78283600-78300800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:78283800-78301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:78285400-78304400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:78285800-78299200	Strong transcription	Fetal Intestine Large	intestine
7	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:78287800-78297400	Weak transcription	A549	lung
11	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr15:78288600-78297000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:78288600-78303000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:78288600-78304400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
19	chr15:78288800-78304800	Weak transcription	Fetal Kidney	kidney
20	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr15:78289000-78309800	Strong transcription	Primary T cells from cord blood	blood
23	chr15:78289400-78299200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:78289400-78309800	Strong transcription	Dnd41	blood
25	chr15:78291800-78302400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:78293000-78298800	Strong transcription	Primary B cells from cord blood	blood
27	chr15:78293200-78297000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:78293200-78309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:78293600-78310000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr15:78293800-78297200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:78293800-78309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:78294000-78297800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:78294000-78299200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:78294200-78299200	Weak transcription	Small Intestine	intestine
35	chr15:78294400-78300800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:78295200-78297400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:78295200-78301200	Genic enhancers	Fetal Thymus	thymus
38	chr15:78295400-78296800	Genic enhancers	Fetal Muscle Leg	muscle
39	chr15:78295400-78297000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr15:78295400-78297000	Enhancers	Psoas Muscle	Psoas
41	chr15:78295400-78297800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:78295400-78298200	Weak transcription	NHEK	skin
43	chr15:78295600-78296800	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr15:78295600-78298600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:78295600-78300200	Weak transcription	Aorta	Aorta
46	chr15:78295600-78301000	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:78295600-78301400	Genic enhancers	Gastric	stomach
48	chr15:78295600-78305600	Enhancers	Pancreas	Pancrea
49	chr15:78295800-78296800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:78295800-78296800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links