Variant report

Variant	rs1145073
Chromosome Location	chr15:45705571-45705572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45694112..45696138-chr15:45705317..45708361,4	MCF-7	breast:
2	chr15:45693480..45696046-chr15:45703264..45708561,5	K562	blood:
3	chr15:45700129..45702415-chr15:45703429..45706303,3	K562	blood:
4	chr15:45703526..45706470-chr15:45707247..45708978,3	K562	blood:
5	chr15:45693239..45696854-chr15:45704414..45708770,8	K562	blood:
6	chr15:45698135..45700009-chr15:45705389..45707645,2	K562	blood:

Variant related genes	Relation type
ENSG00000171766	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10519020	1.00[MEX][hapmap]
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]
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	0.82[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153834	1.00[MEX][hapmap]
rs1153848	0.83[AMR][1000 genomes]
rs1153850	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153851	0.83[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153856	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153859	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1288861	0.93[LWK][hapmap];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]
rs16940734	1.00[MEX][hapmap]
rs16941118	0.85[GIH][hapmap]
rs16941127	0.85[GIH][hapmap]
rs16941188	1.00[MEX][hapmap]
rs16941213	1.00[MEX][hapmap]
rs16941242	1.00[MEX][hapmap]
rs16941245	0.85[GIH][hapmap]
rs16942796	0.85[GIH][hapmap]
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]
rs1706799	0.80[LWK][hapmap]
rs1719242	1.00[EUR][1000 genomes]
rs1719249	0.85[GIH][hapmap];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	0.81[YRI][hapmap];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	0.82[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433605	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];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]
rs2433621	1.00[MEX][hapmap]
rs2453526	1.00[MEX][hapmap]
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[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];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	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486282	1.00[MEX][hapmap]
rs2486287	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2486289	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486290	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]
rs9972443	0.85[GIH][hapmap]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1145073	SPATA5L1	cis	multi-tissue	Pritchard
rs1145073	SPATA5L1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45696200-45707400	Weak transcription	Small Intestine	intestine
2	chr15:45696200-45712800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:45696600-45711000	Weak transcription	Stomach Mucosa	stomach
4	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:45696800-45706000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:45697000-45711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:45697200-45706000	Strong transcription	Brain Substantia Nigra	brain
11	chr15:45697200-45706400	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:45697200-45712400	Strong transcription	Placenta	Placenta
13	chr15:45697200-45713800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr15:45697200-45714200	Strong transcription	Osteobl	bone
15	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:45697400-45705800	Strong transcription	Fetal Intestine Large	intestine
18	chr15:45697400-45712000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:45697400-45713400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:45697400-45713600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:45697400-45714600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:45697400-45714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:45697400-45715200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:45697400-45715200	Strong transcription	Adipose Nuclei	Adipose
25	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr15:45697600-45706000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:45697600-45706000	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr15:45697600-45710000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr15:45697600-45712800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr15:45697600-45713400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:45697600-45714800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:45697600-45715200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:45697600-45715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:45697600-45715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:45697600-45715200	Strong transcription	Fetal Thymus	thymus
38	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:45697800-45707000	Strong transcription	Fetal Lung	lung
40	chr15:45697800-45707200	Strong transcription	Brain Angular Gyrus	brain
41	chr15:45697800-45714200	Strong transcription	HMEC	breast
42	chr15:45697800-45714600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:45697800-45714800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:45697800-45715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:45697800-45716000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:45697800-45716400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:45698000-45707000	Strong transcription	Primary B cells from cord blood	blood
50	chr15:45698000-45714600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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