Variant report

Variant	rs2486290
Chromosome Location	chr15:45709109-45709110
allele	A/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	GATA1	chr15:45708770-45710346	K562	blood:	n/a	chr15:45710190-45710197

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45707965..45711032-chr15:45722401..45726088,3	MCF-7	breast:

Variant related genes	Relation type
SPATA5L1	TF binding region
ENSG00000211519	Chromatin interaction
ENSG00000166920	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1055395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070455	1.00[EUR][1000 genomes]
rs1145072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145073	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145075	0.83[AMR][1000 genomes]
rs1145082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145092	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145094	0.81[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153848	0.83[AMR][1000 genomes]
rs1153850	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153851	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153856	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153859	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1288861	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1346265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1403319	1.00[EUR][1000 genomes]
rs1464558	1.00[EUR][1000 genomes]
rs1706775	1.00[EUR][1000 genomes]
rs1706782	1.00[EUR][1000 genomes]
rs1706783	1.00[EUR][1000 genomes]
rs1706784	1.00[EUR][1000 genomes]
rs1706786	1.00[EUR][1000 genomes]
rs1706788	1.00[EUR][1000 genomes]
rs1706789	1.00[EUR][1000 genomes]
rs1706790	1.00[EUR][1000 genomes]
rs1706794	1.00[EUR][1000 genomes]
rs1706795	1.00[EUR][1000 genomes]
rs1706796	1.00[EUR][1000 genomes]
rs1706797	1.00[EUR][1000 genomes]
rs1719242	1.00[EUR][1000 genomes]
rs1719249	1.00[EUR][1000 genomes]
rs1834686	0.83[AMR][1000 genomes]
rs1874318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2217121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2413765	0.83[AMR][1000 genomes]
rs2433602	0.84[AFR][1000 genomes]
rs2433603	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433604	0.81[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433610	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453546	0.90[AFR][1000 genomes]
rs2453547	0.83[AMR][1000 genomes]
rs2461704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2461706	0.88[AFR][1000 genomes]
rs2467852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467855	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467857	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467859	0.83[AMR][1000 genomes]
rs2486271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486287	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs2486289	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2668740	1.00[EUR][1000 genomes]
rs2687513	1.00[EUR][1000 genomes]
rs57553327	1.00[EUR][1000 genomes]
rs7163395	1.00[EUR][1000 genomes]
rs7163751	1.00[EUR][1000 genomes]
rs7164252	1.00[EUR][1000 genomes]
rs7169175	1.00[EUR][1000 genomes]
rs7173541	1.00[EUR][1000 genomes]
rs7179186	1.00[EUR][1000 genomes]
rs7179844	1.00[EUR][1000 genomes]
rs74009622	1.00[EUR][1000 genomes]
rs8024550	0.83[AMR][1000 genomes]
rs8028061	1.00[EUR][1000 genomes]
rs8033329	1.00[EUR][1000 genomes]
rs8040380	1.00[EUR][1000 genomes]
rs9806260	1.00[EUR][1000 genomes]
rs9972564	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2486290	SPATA5L1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45696200-45712800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:45696600-45711000	Weak transcription	Stomach Mucosa	stomach
3	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:45697000-45711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:45697200-45712400	Strong transcription	Placenta	Placenta
9	chr15:45697200-45713800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr15:45697200-45714200	Strong transcription	Osteobl	bone
11	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:45697400-45712000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:45697400-45713400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:45697400-45713600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:45697400-45714600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:45697400-45714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:45697400-45715200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:45697400-45715200	Strong transcription	Adipose Nuclei	Adipose
20	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:45697600-45710000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr15:45697600-45712800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr15:45697600-45713400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:45697600-45714800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:45697600-45715200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:45697600-45715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:45697600-45715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:45697600-45715200	Strong transcription	Fetal Thymus	thymus
31	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:45697800-45714200	Strong transcription	HMEC	breast
33	chr15:45697800-45714600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:45697800-45714800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:45697800-45715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:45697800-45716000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr15:45697800-45716400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:45698000-45714600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:45698000-45715200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:45698000-45715200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:45698200-45713200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:45698600-45716200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:45699000-45712000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr15:45699000-45712600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:45699000-45713800	Strong transcription	Fetal Brain Female	brain
48	chr15:45699200-45714800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:45699200-45715400	Strong transcription	Brain Germinal Matrix	brain
50	chr15:45700400-45712200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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