Variant report

Variant	rs4794817
Chromosome Location	chr17:37794351-37794352
allele	A/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37792734..37794533-chr17:37886471..37888127,2	K562	blood:
2	chr17:37783631..37786796-chr17:37794221..37796615,3	K562	blood:
3	chr17:37793295..37796255-chr17:37843602..37845450,3	K562	blood:
4	chr17:37792417..37794971-chr17:37842551..37845979,3	MCF-7	breast:
5	chr17:37793727..37796192-chr17:37829753..37832726,2	MCF-7	breast:
6	chr17:37793229..37795498-chr17:37814501..37816101,2	MCF-7	breast:
7	chr17:37791351..37794497-chr17:37895466..37898659,4	MCF-7	breast:
8	chr17:37790905..37794856-chr17:37820000..37822270,4	K562	blood:
9	chr17:37791520..37796368-chr17:37822308..37826994,8	K562	blood:
10	chr17:37793922..37796197-chr17:37796263..37800246,4	MCF-7	breast:
11	chr17:37792754..37795170-chr17:37883979..37887971,4	K562	blood:
12	chr17:37762236..37764592-chr17:37791810..37794599,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141744	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000131771	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000171532	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000173991	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1018246	0.88[ASN][1000 genomes]
rs1053651	0.92[ASN][1000 genomes]
rs10852934	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651497	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11658786	0.89[ASN][1000 genomes]
rs11869286	0.91[ASN][1000 genomes]
rs12150298	0.88[ASN][1000 genomes]
rs12150603	0.88[ASN][1000 genomes]
rs12453682	0.89[ASN][1000 genomes]
rs12940986	0.89[ASN][1000 genomes]
rs14050	0.88[ASN][1000 genomes]
rs1476278	0.89[ASN][1000 genomes]
rs1495099	1.00[ASN][1000 genomes]
rs1495100	0.88[ASN][1000 genomes]
rs1495101	0.88[ASN][1000 genomes]
rs1495102	0.88[ASN][1000 genomes]
rs1565920	0.87[ASN][1000 genomes]
rs1565922	0.88[ASN][1000 genomes]
rs1874228	0.98[ASN][1000 genomes]
rs1877031	0.91[ASN][1000 genomes]
rs2247862	0.88[ASN][1000 genomes]
rs2271308	0.89[ASN][1000 genomes]
rs2271309	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2313171	0.88[ASN][1000 genomes]
rs2517952	0.81[ASN][1000 genomes]
rs2517953	0.83[ASN][1000 genomes]
rs2517954	0.82[ASN][1000 genomes]
rs2517955	0.81[ASN][1000 genomes]
rs2517956	0.81[ASN][1000 genomes]
rs2517957	0.89[ASN][1000 genomes]
rs2517958	0.89[ASN][1000 genomes]
rs2517959	0.82[ASN][1000 genomes]
rs2517960	0.80[ASN][1000 genomes]
rs2934951	0.88[ASN][1000 genomes]
rs2934952	0.88[ASN][1000 genomes]
rs2934953	0.88[ASN][1000 genomes]
rs2934956	0.88[ASN][1000 genomes]
rs2941503	0.88[ASN][1000 genomes]
rs2941504	0.89[ASN][1000 genomes]
rs2941505	0.88[ASN][1000 genomes]
rs2941506	0.88[ASN][1000 genomes]
rs2952151	0.88[ASN][1000 genomes]
rs2952152	0.87[ASN][1000 genomes]
rs33953566	0.99[ASN][1000 genomes]
rs3751903	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764352	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764353	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794712	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817160	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407307	0.85[ASN][1000 genomes]
rs4795388	0.93[ASN][1000 genomes]
rs4795389	0.98[ASN][1000 genomes]
rs4795390	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs732083	0.88[ASN][1000 genomes]
rs732084	0.88[ASN][1000 genomes]
rs8077172	0.88[ASN][1000 genomes]
rs8078228	0.88[ASN][1000 genomes]
rs879606	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881844	0.87[ASN][1000 genomes]
rs903501	0.89[ASN][1000 genomes]
rs903502	0.87[ASN][1000 genomes]
rs907087	0.88[ASN][1000 genomes]
rs907088	0.88[ASN][1000 genomes]
rs907089	0.88[ASN][1000 genomes]
rs907090	0.88[ASN][1000 genomes]
rs907094	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303274	0.89[ASN][1000 genomes]
rs9675194	0.88[ASN][1000 genomes]
rs9915323	0.92[ASN][1000 genomes]
rs9972882	0.84[AFR][1000 genomes];0.92[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	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4794817	PGAP3	cis	Thyroid	GTEx
rs4794817	PGAP3	cis	Stomach	GTEx
rs4794817	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37792400-37795200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:37792600-37795200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:37792800-37794400	Active TSS	Right Atrium	heart
4	chr17:37792800-37794600	Active TSS	Ovary	ovary
5	chr17:37792800-37794800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr17:37793000-37794400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr17:37793000-37794400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:37793000-37794400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:37793000-37794400	Active TSS	NHDF-Ad	bronchial
10	chr17:37793000-37794800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:37793200-37794400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:37793200-37794400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr17:37793200-37794400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr17:37793200-37795000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr17:37793400-37794400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr17:37793400-37794400	Active TSS	Gastric	stomach
17	chr17:37793600-37794400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr17:37793600-37794600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
19	chr17:37793600-37794800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr17:37793800-37794400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr17:37793800-37794400	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr17:37793800-37794400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr17:37793800-37794600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:37793800-37794600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:37793800-37794600	Flanking Active TSS	HUVEC	blood vessel
26	chr17:37793800-37794800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr17:37793800-37794800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr17:37793800-37794800	Flanking Active TSS	Liver	Liver
29	chr17:37793800-37794800	Flanking Active TSS	Colonic Mucosa	Colon
30	chr17:37793800-37794800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr17:37793800-37794800	Flanking Active TSS	Stomach Mucosa	stomach
32	chr17:37793800-37794800	Flanking Active TSS	Hela-S3	cervix
33	chr17:37793800-37795000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr17:37793800-37795000	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr17:37793800-37795200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr17:37793800-37795200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr17:37793800-37795200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:37793800-37795200	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr17:37793800-37795200	Flanking Active TSS	K562	blood
40	chr17:37794000-37794400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr17:37794000-37794400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:37794000-37794400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr17:37794000-37794400	Flanking Active TSS	Placenta	Placenta
44	chr17:37794000-37794400	Flanking Active TSS	Fetal Stomach	stomach
45	chr17:37794000-37794400	Flanking Active TSS	Left Ventricle	heart
46	chr17:37794000-37794400	Flanking Active TSS	Pancreas	Pancrea
47	chr17:37794000-37794400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr17:37794000-37794600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:37794000-37794600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr17:37794000-37794600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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