Variant report

Variant	rs59499270
Chromosome Location	chr15:78296470-78296471
allele	G/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	REST	chr15:78296448-78296861	GM12878	blood:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
2	POLR2A	chr15:78296326-78297011	GM12878	blood:	n/a	n/a
3	REST	chr15:78296470-78296891	U87	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
4	REST	chr15:78296427-78296983	ECC-1	luminal epithelium:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
5	REST	chr15:78296463-78296881	PFSK-1	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
6	REST	chr15:78296446-78296888	MCF-7	breast:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
7	NR2F2	chr15:78295654-78296507	MCF-7	breast:	n/a	n/a
8	REST	chr15:78296457-78296831	H1-hESC	embryonic stem cell:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
9	REST	chr15:78296403-78296888	ECC-1	luminal epithelium:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
10	REST	chr15:78296391-78296876	MCF-7	breast:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
11	REST	chr15:78296431-78296904	PFSK-1	brain:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
12	REST	chr15:78296333-78296825	A549	lung:	n/a	chr15:78296681-78296690 chr15:78296682-78296695 chr15:78296769-78296782 chr15:78296675-78296695
13	MAX	chr15:78295686-78296829	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11858138	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16953970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16969397	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969464	1.00[AMR][1000 genomes]
rs57993009	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58416217	1.00[AMR][1000 genomes]
rs61183047	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61596558	0.89[AMR][1000 genomes]
rs8030999	0.90[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:123 , 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	chr15:78289800-78296600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:78291800-78302400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:78293000-78298800	Strong transcription	Primary B cells from cord blood	blood
28	chr15:78293200-78296600	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr15:78293200-78296600	Strong transcription	Colonic Mucosa	Colon
30	chr15:78293200-78297000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:78293200-78309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:78293400-78296600	Strong transcription	Placenta	Placenta
33	chr15:78293600-78310000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr15:78293800-78297200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:78293800-78309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:78294000-78296600	Weak transcription	Brain Substantia Nigra	brain
37	chr15:78294000-78297800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:78294000-78299200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:78294200-78296600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:78294200-78299200	Weak transcription	Small Intestine	intestine
41	chr15:78294400-78300800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:78295000-78296600	Strong transcription	Esophagus	oesophagus
43	chr15:78295200-78297400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:78295200-78301200	Genic enhancers	Fetal Thymus	thymus
45	chr15:78295400-78296800	Genic enhancers	Fetal Muscle Leg	muscle
46	chr15:78295400-78297000	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr15:78295400-78297000	Enhancers	Psoas Muscle	Psoas
48	chr15:78295400-78297800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:78295400-78298200	Weak transcription	NHEK	skin
50	chr15:78295600-78296800	Genic enhancers	Rectal Mucosa Donor 29	rectum

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