Variant report

Variant	rs2606133
Chromosome Location	chr15:52045115-52045116
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	SPI1	chr15:52045035-52045655	HL-60	blood:	n/a	n/a
2	MXI1	chr15:52042784-52045538	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr15:52045013-52045213	SH-SY5Y	brain:	n/a	chr15:52045169-52045186
4	GATA2	chr15:52045044-52045305	SH-SY5Y	brain:	n/a	chr15:52045169-52045186

No.	Distal block	Cell Line	Cell type
1	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
2	chr15:51913469..51917109-chr15:52042794..52045514,3	MCF-7	breast:
3	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
4	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

Variant related genes	Relation type
LYSMD2	TF binding region
ENSG00000140280	Chromatin interaction
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1133878	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[ASN][1000 genomes]
rs16964483	1.00[ASN][1000 genomes]
rs17611465	1.00[ASN][1000 genomes]
rs1863429	0.81[AMR][1000 genomes]
rs1972419	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2016057	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448810	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2554354	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570230	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	1.00[ASN][1000 genomes]
rs2606128	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2606130	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[ASN][1000 genomes]
rs2623245	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623258	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs691738	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2606133	RP11-707P17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52043000-52045200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:52043200-52045200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr15:52043400-52045200	Active TSS	Brain Cingulate Gyrus	brain
4	chr15:52043400-52045200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:52043600-52045200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr15:52043600-52045200	Bivalent/Poised TSS	Fetal Stomach	stomach
7	chr15:52044200-52045800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr15:52044400-52045200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr15:52044400-52045200	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr15:52044400-52045200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:52044400-52045200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:52044400-52045200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr15:52044400-52045800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:52044400-52046400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr15:52044400-52050800	Weak transcription	Gastric	stomach
16	chr15:52044600-52045200	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr15:52044600-52045200	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr15:52044600-52045200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr15:52044600-52045200	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr15:52044600-52045400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:52044600-52045400	Enhancers	Left Ventricle	heart
22	chr15:52044600-52045600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr15:52044600-52045600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr15:52044600-52046800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr15:52044600-52060000	Weak transcription	Esophagus	oesophagus
26	chr15:52044600-52060200	Weak transcription	Aorta	Aorta
27	chr15:52044800-52045200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:52044800-52045200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr15:52044800-52045200	Flanking Active TSS	Dnd41	blood
30	chr15:52044800-52045400	Enhancers	Duodenum Mucosa	Duodenum
31	chr15:52044800-52045600	Enhancers	K562	blood
32	chr15:52044800-52046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:52044800-52046800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr15:52044800-52047600	Weak transcription	Placenta	Placenta
35	chr15:52044800-52047600	Weak transcription	Lung	lung
36	chr15:52044800-52047800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:52044800-52049800	Weak transcription	Psoas Muscle	Psoas
38	chr15:52044800-52050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:52044800-52051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:52044800-52051000	Weak transcription	Right Ventricle	heart
41	chr15:52044800-52060000	Weak transcription	Spleen	Spleen
42	chr15:52045000-52045200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:52045000-52045200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:52045000-52045200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr15:52045000-52045200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:52045000-52045200	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:52045000-52045200	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr15:52045000-52045200	Active TSS	Brain Germinal Matrix	brain
49	chr15:52045000-52045400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr15:52045000-52045400	Enhancers	Cortex derived primary cultured neurospheres	brain

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