Variant report

Variant	rs2486288
Chromosome Location	chr15:45712339-45712340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45698341..45701753-chr15:45711661..45714257,4	K562	blood:
2	chr15:45693902..45696245-chr15:45709725..45712520,2	K562	blood:
3	chr15:45698341..45700886-chr15:45711508..45714257,3	K562	blood:

Variant related genes	Relation type
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1049518	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145086	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145089	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145093	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145097	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153845	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1153855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153860	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153862	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636114	0.88[AMR][1000 genomes]
rs11855414	0.90[AMR][1000 genomes]
rs12909409	0.90[AMR][1000 genomes]
rs12910764	0.90[AMR][1000 genomes]
rs1346267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547487	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1617634	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1617984	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1719245	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1719246	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2002035	0.86[AMR][1000 genomes]
rs2015295	0.85[AMR][1000 genomes]
rs2433601	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2433616	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2453533	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461700	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461701	0.80[AFR][1000 genomes]
rs2467853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467858	0.80[AFR][1000 genomes]
rs2467862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467865	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899375	0.88[AMR][1000 genomes]
rs35861938	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872192	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9921008	0.86[AMR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2486288	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2486288	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2486288	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2486288	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs2486288	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2486288	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2486288	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2486288	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2486288	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2486288	CTD-2651B20.3	cis	lung	GTEx
rs2486288	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2486288	CTD-2651B20.3	cis	Thyroid	GTEx
rs2486288	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs2486288	CTD-2651B20.3	cis	Muscle Skeletal	GTEx

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	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:45697200-45712400	Strong transcription	Placenta	Placenta
7	chr15:45697200-45713800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr15:45697200-45714200	Strong transcription	Osteobl	bone
9	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:45697400-45713400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:45697400-45713600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:45697400-45714600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:45697400-45714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:45697400-45715200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:45697400-45715200	Strong transcription	Adipose Nuclei	Adipose
17	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:45697600-45712800	Strong transcription	Brain Cingulate Gyrus	brain
21	chr15:45697600-45713400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:45697600-45714800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:45697600-45715200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:45697600-45715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:45697600-45715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:45697600-45715200	Strong transcription	Fetal Thymus	thymus
27	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:45697800-45714200	Strong transcription	HMEC	breast
29	chr15:45697800-45714600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:45697800-45714800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:45697800-45715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:45697800-45716000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:45697800-45716400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:45698000-45714600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:45698000-45715200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:45698000-45715200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:45698200-45713200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:45698600-45716200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:45699000-45712600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:45699000-45713800	Strong transcription	Fetal Brain Female	brain
43	chr15:45699200-45714800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:45699200-45715400	Strong transcription	Brain Germinal Matrix	brain
45	chr15:45700400-45714800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:45700800-45713400	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:45700800-45714800	Strong transcription	HSMMtube	muscle
48	chr15:45702600-45713400	Strong transcription	Left Ventricle	heart
49	chr15:45704800-45714800	Strong transcription	NH-A	brain
50	chr15:45705200-45712600	Strong transcription	Colon Smooth Muscle	Colon

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