Variant report

Variant	rs9806699
Chromosome Location	chr15:45740392-45740393
allele	A/G
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	MAZ	chr15:45740256-45741095	Hela-S3	cervix:	n/a	chr15:45740646-45740656
2	SMC3	chr15:45740273-45740550	Hela-S3	cervix:	n/a	n/a
3	CHD2	chr15:45740237-45740640	Hela-S3	cervix:	n/a	n/a
4	FOS	chr15:45740346-45740549	MCF10A-Er-Src	breast:	n/a	chr15:45740462-45740472 chr15:45740463-45740471
5	FOS	chr15:45740286-45740560	MCF10A-Er-Src	breast:	n/a	chr15:45740462-45740472 chr15:45740463-45740471
6	MAZ	chr15:45740084-45741150	IMR90	lung:	n/a	chr15:45740646-45740656
7	ZNF143	chr15:45740302-45740548	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:45740180-45740732	Hela-S3	cervix:	n/a	n/a
9	MAX	chr15:45740256-45741043	Hela-S3	cervix:	n/a	chr15:45740646-45740656
10	ESR1	chr15:45740224-45740529	ECC-1	luminal epithelium:	n/a	chr15:45740396-45740411 chr15:45740395-45740412 chr15:45740433-45740448 chr15:45740396-45740413
11	CEBPB	chr15:45740235-45740650	Hela-S3	cervix:	n/a	n/a
12	FOS	chr15:45740353-45740476	MCF10A-Er-Src	breast:	n/a	chr15:45740462-45740472 chr15:45740463-45740471
13	SMARCC1	chr15:45740184-45741352	Hela-S3	cervix:	n/a	chr15:45740463-45740472
14	EBF1	chr15:45740179-45740664	GM12878	blood:	n/a	n/a
15	USF2	chr15:45740200-45740486	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr15:45740270-45740734	IMR90	lung:	n/a	n/a
17	EBF1	chr15:45740218-45740633	GM12878	blood:	n/a	n/a
18	CEBPB	chr15:45740352-45740607	A549	lung:	n/a	n/a
19	RCOR1	chr15:45740266-45740592	Hela-S3	cervix:	n/a	n/a
20	MAFK	chr15:45740386-45740556	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45736069..45742318-chr15:45926037..45929619,6	MCF-7	breast:
2	chr15:45693986..45696362-chr15:45736299..45740535,4	MCF-7	breast:

Variant related genes	Relation type
RNU7-5P	TF binding region
ENSG00000259354	TF binding region
ENSG00000137767	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10444821	0.82[CEU][hapmap]
rs1049508	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs10519022	0.81[CEU][hapmap]
rs1145091	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs1153849	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs1153858	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs12437840	0.81[CEU][hapmap]
rs12437887	0.81[CEU][hapmap]
rs12440038	0.81[CEU][hapmap]
rs1288775	0.82[CEU][hapmap]
rs1346266	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs1346268	0.81[CEU][hapmap]
rs1365610	0.81[CEU][hapmap]
rs1554521	0.81[CEU][hapmap]
rs16943246	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1719247	0.84[GIH][hapmap]
rs1820518	0.81[CEU][hapmap]
rs1974981	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056493	0.82[CEU][hapmap]
rs2066090	0.82[CEU][hapmap]
rs28569043	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759899	0.81[CEU][hapmap]
rs3809472	0.81[CEU][hapmap]
rs4395020	0.81[CEU][hapmap]
rs4627277	0.82[CEU][hapmap]
rs4774580	0.81[CEU][hapmap]
rs4775911	0.81[CEU][hapmap]
rs7164602	0.81[CEU][hapmap]
rs7171577	0.82[CEU][hapmap]
rs8032904	0.81[CEU][hapmap]

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	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
4	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
5	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
6	nsv442701	chr15:45737096-45748752	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9806699	SPATA5L1	cis	lung	GTEx
rs9806699	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs9806699	SPATA5L1	cis	Esophagus Muscularis	GTEx
rs9806699	SPATA5L1	cis	Whole Blood	GTEx
rs9806699	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs9806699	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs9806699	SPATA5L1	cis	Thyroid	GTEx
rs9806699	SPATA5L1	cis	Nerve Tibial	GTEx
rs9806699	CTD-2651B20.3	cis	Thyroid	GTEx
rs9806699	CTD-2651B20.4	cis	Nerve Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45731400-45740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:45735200-45740400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:45735200-45740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:45738200-45740400	Weak transcription	HMEC	breast
5	chr15:45738200-45746600	Weak transcription	Osteobl	bone
6	chr15:45738400-45740400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:45738400-45740400	Weak transcription	Spleen	Spleen
8	chr15:45738400-45740400	Weak transcription	GM12878-XiMat	blood
9	chr15:45738400-45740600	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr15:45738400-45740600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr15:45738400-45742000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:45738400-45742000	Enhancers	Stomach Mucosa	stomach
13	chr15:45739000-45740400	Weak transcription	Fetal Intestine Large	intestine
14	chr15:45739000-45740400	Weak transcription	Fetal Intestine Small	intestine
15	chr15:45739000-45740400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:45739000-45741400	Weak transcription	Liver	Liver
17	chr15:45739200-45742000	Weak transcription	Pancreas	Pancrea
18	chr15:45739400-45740400	Weak transcription	Colonic Mucosa	Colon
19	chr15:45739400-45740800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:45739600-45740600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr15:45740000-45740800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:45740000-45741600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:45740200-45740400	Enhancers	Hela-S3	cervix
24	chr15:45740200-45740600	Enhancers	A549	lung
25	chr15:45740200-45740800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:45740200-45740800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:45740200-45740800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:45740200-45740800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr15:45740200-45741000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:45740200-45741000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:45740200-45741000	Enhancers	Esophagus	oesophagus
32	chr15:45740200-45741000	Enhancers	Lung	lung
33	chr15:45740200-45741000	Enhancers	Small Intestine	intestine
34	chr15:45740200-45741000	Enhancers	HSMMtube	muscle
35	chr15:45740200-45741000	Enhancers	NHDF-Ad	bronchial
36	chr15:45740200-45741200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:45740200-45741200	Enhancers	NH-A	brain
38	chr15:45740200-45741400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:45740200-45741400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:45740200-45741400	Enhancers	Placenta	Placenta
41	chr15:45740200-45741400	Enhancers	Gastric	stomach
42	chr15:45740200-45741600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:45740200-45742000	Enhancers	Duodenum Mucosa	Duodenum

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