Variant report

Variant	rs1565920
Chromosome Location	chr17:37831613-37831614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37827266..37833048-chr17:37842420..37846685,6	MCF-7	breast:
2	chr17:37831185..37834082-chr17:37834378..37836489,3	MCF-7	breast:
3	chr17:37829376..37831831-chr17:37883917..37885766,2	K562	blood:
4	chr17:37793727..37796192-chr17:37829753..37832726,2	MCF-7	breast:
5	chr17:37829760..37835390-chr17:37853762..37858979,8	MCF-7	breast:
6	chr17:37806036..37809512-chr17:37829090..37833058,4	K562	blood:
7	chr17:37829190..37831806-chr17:37886312..37888416,2	MCF-7	breast:
8	chr17:37829895..37831934-chr17:37839264..37841541,2	MCF-7	breast:
9	chr17:37824143..37826951-chr17:37830490..37832127,2	MCF-7	breast:
10	chr17:37831092..37832892-chr17:37842525..37844810,2	MCF-7	breast:
11	chr17:37830304..37832769-chr17:37860083..37864558,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000141741	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1018246	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053651	0.94[ASN][1000 genomes]
rs10852934	0.87[ASN][1000 genomes]
rs11651497	0.87[ASN][1000 genomes]
rs11658786	0.91[ASN][1000 genomes]
rs11869286	0.94[ASN][1000 genomes]
rs12150298	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150603	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940986	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14050	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495099	0.87[ASN][1000 genomes]
rs1495100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495101	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495102	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565922	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874228	0.85[ASN][1000 genomes]
rs1877031	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2247862	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271308	0.91[ASN][1000 genomes]
rs2271309	0.87[ASN][1000 genomes]
rs2313171	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517951	0.84[AMR][1000 genomes]
rs2517952	0.90[ASN][1000 genomes]
rs2517953	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517954	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517955	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517956	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517957	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517958	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517959	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517960	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934951	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934952	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934953	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934956	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941503	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941504	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941505	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941506	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952151	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952152	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33953566	0.87[ASN][1000 genomes]
rs35734596	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751903	0.87[ASN][1000 genomes]
rs3764352	0.87[ASN][1000 genomes]
rs3764353	0.87[ASN][1000 genomes]
rs3794712	0.83[ASN][1000 genomes]
rs3817160	0.87[ASN][1000 genomes]
rs407307	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794817	0.87[ASN][1000 genomes]
rs4795388	0.81[ASN][1000 genomes]
rs4795389	0.85[ASN][1000 genomes]
rs4795390	0.87[ASN][1000 genomes]
rs732083	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732084	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8077172	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8078228	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879606	0.87[ASN][1000 genomes]
rs881844	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs903501	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903502	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907087	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907088	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907089	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907090	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907094	0.87[ASN][1000 genomes]
rs9303274	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9675194	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9972882	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv908215	chr17:37818561-37834541	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	esv1848656	chr17:37830900-37834998	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1565920	PGAP3	cis	Heart Left Ventricle	GTEx
rs1565920	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs1565920	PGAP3	cis	Muscle Skeletal	GTEx
rs1565920	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs1565920	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs1565920	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37824800-37833200	Enhancers	Fetal Heart	heart
2	chr17:37825200-37832600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:37825200-37833000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:37825800-37833000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:37826400-37833000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:37827600-37832800	Enhancers	Fetal Intestine Large	intestine
7	chr17:37827800-37837800	Genic enhancers	Fetal Intestine Small	intestine
8	chr17:37828400-37832000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:37828400-37832200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:37828400-37832400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:37828400-37832600	Weak transcription	Fetal Brain Female	brain
12	chr17:37828400-37834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:37828400-37834200	Weak transcription	Fetal Kidney	kidney
14	chr17:37828600-37831800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:37828600-37831800	Weak transcription	Adipose Nuclei	Adipose
16	chr17:37828600-37832000	Weak transcription	Liver	Liver
17	chr17:37828600-37832200	Weak transcription	Brain Angular Gyrus	brain
18	chr17:37828600-37832200	Weak transcription	Brain Substantia Nigra	brain
19	chr17:37828600-37833000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr17:37828600-37833200	Weak transcription	Brain Anterior Caudate	brain
21	chr17:37828600-37834200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:37828600-37836000	Weak transcription	Ovary	ovary
23	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:37828800-37831800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr17:37828800-37831800	Weak transcription	Lung	lung
26	chr17:37828800-37832000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:37828800-37832600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr17:37828800-37835400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:37829000-37839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:37829000-37839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:37829200-37833000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:37829400-37832200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:37829400-37834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:37829400-37837400	Enhancers	Primary B cells from cord blood	blood
36	chr17:37829600-37832200	Weak transcription	Fetal Brain Male	brain
37	chr17:37829600-37835600	Weak transcription	Brain Germinal Matrix	brain
38	chr17:37829600-37837600	Enhancers	Primary B cells from peripheral blood	blood
39	chr17:37829800-37833000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:37829800-37833800	Enhancers	Right Ventricle	heart
41	chr17:37829800-37834000	Strong transcription	Fetal Stomach	stomach
42	chr17:37829800-37835000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr17:37829800-37843600	Weak transcription	NHDF-Ad	bronchial
44	chr17:37830200-37832200	Enhancers	Fetal Muscle Trunk	muscle
45	chr17:37830200-37832400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:37830200-37832400	Enhancers	Placenta	Placenta
47	chr17:37830200-37836800	Enhancers	Stomach Mucosa	stomach
48	chr17:37830400-37832200	Enhancers	Fetal Lung	lung
49	chr17:37830400-37832400	Enhancers	K562	blood
50	chr17:37830400-37832600	Enhancers	Skeletal Muscle Male	skeletal muscle

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