Variant report

Variant	rs11658786
Chromosome Location	chr17:37815899-37815900
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	MTA3	chr17:37815458-37816075	GM12878	blood:	n/a	n/a
2	RUNX3	chr17:37815516-37816013	GM12878	blood:	n/a	n/a
3	SPI1	chr17:37815560-37816089	GM12891	blood:	n/a	chr17:37815691-37815704
4	RUNX3	chr17:37815674-37815951	GM12878	blood:	n/a	n/a
5	SPI1	chr17:37815658-37815939	GM12878	blood:	n/a	chr17:37815691-37815704
6	SPI1	chr17:37815756-37815941	GM12878	blood:	n/a	n/a
7	SPI1	chr17:37815620-37815972	GM12891	blood:	n/a	chr17:37815691-37815704

No.	Distal block	Cell Line	Cell type
1	chr17:37793229..37795498-chr17:37814501..37816101,2	MCF-7	breast:
2	chr17:37815487..37818092-chr17:37864402..37866827,2	MCF-7	breast:
3	chr17:37814865..37817539-chr17:37818088..37820916,2	MCF-7	breast:

Variant related genes	Relation type
STARD3	TF binding region
TCAP	TF binding region
ENSG00000173991	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000141736	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1018246	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1053651	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10852934	0.89[ASN][1000 genomes]
rs11651497	0.89[ASN][1000 genomes]
rs11869286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150298	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150603	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12940986	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14050	0.92[ASN][1000 genomes]
rs1476278	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1495099	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1495100	0.92[ASN][1000 genomes]
rs1495101	0.92[ASN][1000 genomes]
rs1495102	0.92[ASN][1000 genomes]
rs1565920	0.91[ASN][1000 genomes]
rs1565922	0.92[ASN][1000 genomes]
rs1874228	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1877031	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247862	0.92[ASN][1000 genomes]
rs2271308	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2271309	0.89[ASN][1000 genomes]
rs2313171	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517952	0.83[ASN][1000 genomes]
rs2517953	0.86[ASN][1000 genomes]
rs2517954	0.85[ASN][1000 genomes]
rs2517955	0.85[ASN][1000 genomes]
rs2517956	0.85[ASN][1000 genomes]
rs2517957	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517958	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517959	0.85[ASN][1000 genomes]
rs2517960	0.84[ASN][1000 genomes]
rs2934951	0.92[ASN][1000 genomes]
rs2934952	0.92[ASN][1000 genomes]
rs2934953	0.92[ASN][1000 genomes]
rs2934956	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2941503	0.92[ASN][1000 genomes]
rs2941504	0.92[ASN][1000 genomes]
rs2941505	0.92[ASN][1000 genomes]
rs2941506	0.92[ASN][1000 genomes]
rs2952151	0.92[ASN][1000 genomes]
rs2952152	0.90[ASN][1000 genomes]
rs33953566	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35734596	0.83[ASN][1000 genomes]
rs3751903	0.89[ASN][1000 genomes]
rs3764351	0.83[EUR][1000 genomes]
rs3764352	0.89[ASN][1000 genomes]
rs3764353	0.89[ASN][1000 genomes]
rs3794712	0.85[ASN][1000 genomes]
rs3817160	0.89[ASN][1000 genomes]
rs407307	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794817	0.89[ASN][1000 genomes]
rs4795388	0.83[ASN][1000 genomes]
rs4795389	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4795390	0.89[ASN][1000 genomes]
rs732083	0.92[ASN][1000 genomes]
rs732084	0.92[ASN][1000 genomes]
rs8077172	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078228	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs879606	0.89[ASN][1000 genomes]
rs881844	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903501	0.91[ASN][1000 genomes]
rs903502	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907087	0.92[ASN][1000 genomes]
rs907088	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907089	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907090	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907094	0.89[ASN][1000 genomes]
rs9303274	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9675194	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9915323	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9972882	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11658786	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs11658786	PGAP3	cis	lung	GTEx
rs11658786	PGAP3	cis	Thyroid	GTEx
rs11658786	PGAP3	cis	Nerve Tibial	GTEx
rs11658786	PGAP3	cis	Heart Left Ventricle	GTEx
rs11658786	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37795000-37823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:37795400-37818000	Weak transcription	Fetal Kidney	kidney
3	chr17:37799800-37819600	Weak transcription	Osteobl	bone
4	chr17:37800000-37818600	Weak transcription	Hela-S3	cervix
5	chr17:37800000-37820000	Weak transcription	NH-A	brain
6	chr17:37800200-37816800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:37800600-37816200	Weak transcription	NHEK	skin
8	chr17:37801800-37817000	Weak transcription	A549	lung
9	chr17:37803800-37821800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:37808400-37819200	Weak transcription	Small Intestine	intestine
11	chr17:37809200-37816200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:37809800-37816400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:37809800-37819400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:37810000-37817200	Weak transcription	HSMM	muscle
15	chr17:37810000-37819400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:37810000-37819600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr17:37810000-37820000	Weak transcription	HSMMtube	muscle
18	chr17:37810000-37820400	Strong transcription	Brain Germinal Matrix	brain
19	chr17:37810200-37816200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:37810200-37816400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:37810200-37816400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:37810200-37816600	Strong transcription	Spleen	Spleen
23	chr17:37810200-37819800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:37810400-37817600	Weak transcription	Stomach Mucosa	stomach
25	chr17:37810400-37817800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr17:37810600-37818600	Strong transcription	Fetal Intestine Small	intestine
27	chr17:37810600-37819200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:37810600-37819200	Strong transcription	Fetal Intestine Large	intestine
29	chr17:37810600-37820000	Weak transcription	K562	blood
30	chr17:37810600-37821000	Weak transcription	Fetal Brain Male	brain
31	chr17:37810800-37816600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:37810800-37819400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr17:37810800-37819600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:37810800-37820600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr17:37811000-37818000	Strong transcription	Esophagus	oesophagus
36	chr17:37811000-37818600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:37811000-37818600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:37811400-37818600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:37811800-37819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:37811800-37820800	Strong transcription	Fetal Brain Female	brain
41	chr17:37812000-37816400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:37812000-37817600	Strong transcription	Gastric	stomach
43	chr17:37812000-37819400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:37812000-37819600	Genic enhancers	Lung	lung
45	chr17:37812400-37816600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:37812400-37818200	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr17:37812400-37819200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:37812400-37819600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:37812600-37816800	Strong transcription	Colonic Mucosa	Colon
50	chr17:37812600-37818000	Weak transcription	HMEC	breast

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