Variant report

Variant	rs3794712
Chromosome Location	chr17:37791487-37791488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:37791440-37791590	HRE	kidney:	n/a	n/a
2	CTCF	chr17:37791460-37791610	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr17:37791480-37791630	BJ	skin:	n/a	n/a
4	CTCF	chr17:37791460-37791610	GM12864	blood:	n/a	n/a
5	CTCF	chr17:37791480-37791630	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr17:37791440-37791730	K562	blood:	n/a	n/a
7	CTCF	chr17:37791480-37791630	AG10803	skin:	n/a	n/a
8	CTCF	chr17:37791452-37791690	K562	blood:	n/a	n/a
9	CTCF	chr17:37791420-37791570	NHEK	skin:	n/a	n/a
10	CTCF	chr17:37791460-37791610	GM12873	blood:	n/a	n/a
11	CTCF	chr17:37791460-37791610	HCFaa	heart:	n/a	n/a
12	CTCF	chr17:37791480-37791630	BE2_C	brain:	n/a	n/a
13	CTCF	chr17:37791344-37791731	K562	blood:	n/a	n/a
14	CTCF	chr17:37791440-37791590	A549	lung:	n/a	n/a
15	CTCF	chr17:37791480-37791630	WERI-Rb-1	eye:	n/a	n/a
16	CTCF	chr17:37791480-37791630	GM12878	blood:	n/a	n/a
17	CTCF	chr17:37791437-37791751	K562	blood:	n/a	n/a
18	CTCF	chr17:37791480-37791630	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37785506..37788397-chr17:37788916..37793369,4	K562	blood:
2	chr17:37789471..37791960-chr17:37905766..37908053,2	MCF-7	breast:
3	chr17:37791351..37794497-chr17:37895466..37898659,4	MCF-7	breast:
4	chr17:37790905..37794856-chr17:37820000..37822270,4	K562	blood:
5	chr17:37790730..37792254-chr17:37891251..37894000,2	K562	blood:
6	chr17:37789742..37792172-chr17:37795424..37797567,2	MCF-7	breast:
7	chr17:37789315..37792571-chr17:37910228..37913282,4	K562	blood:

No data

Variant related genes	Relation type
STARD3	TF binding region
ENSG00000131771	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000173991	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1018246	0.84[ASN][1000 genomes]
rs1053651	0.88[ASN][1000 genomes]
rs10852934	0.95[ASN][1000 genomes]
rs11651497	0.97[ASN][1000 genomes]
rs11658786	0.85[ASN][1000 genomes]
rs11869286	0.87[ASN][1000 genomes]
rs12150298	0.84[ASN][1000 genomes]
rs12150603	0.84[ASN][1000 genomes]
rs12453682	0.87[ASN][1000 genomes]
rs12940986	0.85[ASN][1000 genomes]
rs14050	0.84[ASN][1000 genomes]
rs1476278	0.85[ASN][1000 genomes]
rs1495099	0.96[ASN][1000 genomes]
rs1495100	0.84[ASN][1000 genomes]
rs1495101	0.84[ASN][1000 genomes]
rs1495102	0.84[ASN][1000 genomes]
rs1565920	0.83[ASN][1000 genomes]
rs1565922	0.84[ASN][1000 genomes]
rs1874228	0.94[ASN][1000 genomes]
rs1877031	0.87[ASN][1000 genomes]
rs2247862	0.84[ASN][1000 genomes]
rs2271308	0.85[ASN][1000 genomes]
rs2271309	0.96[ASN][1000 genomes]
rs2313171	0.84[ASN][1000 genomes]
rs2517957	0.85[ASN][1000 genomes]
rs2517958	0.85[ASN][1000 genomes]
rs2934951	0.84[ASN][1000 genomes]
rs2934952	0.84[ASN][1000 genomes]
rs2934953	0.84[ASN][1000 genomes]
rs2934956	0.84[ASN][1000 genomes]
rs2941503	0.84[ASN][1000 genomes]
rs2941504	0.85[ASN][1000 genomes]
rs2941505	0.84[ASN][1000 genomes]
rs2941506	0.84[ASN][1000 genomes]
rs2952151	0.84[ASN][1000 genomes]
rs2952152	0.83[ASN][1000 genomes]
rs33953566	0.95[ASN][1000 genomes]
rs3751903	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764352	0.97[ASN][1000 genomes]
rs3764353	0.97[ASN][1000 genomes]
rs3817160	0.96[ASN][1000 genomes]
rs407307	0.81[ASN][1000 genomes]
rs4794817	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795388	0.89[ASN][1000 genomes]
rs4795389	0.94[ASN][1000 genomes]
rs4795390	0.95[ASN][1000 genomes]
rs732083	0.84[ASN][1000 genomes]
rs732084	0.84[ASN][1000 genomes]
rs8077172	0.84[ASN][1000 genomes]
rs8078228	0.84[ASN][1000 genomes]
rs879606	0.95[ASN][1000 genomes]
rs881844	0.83[ASN][1000 genomes]
rs903501	0.85[ASN][1000 genomes]
rs903502	0.83[ASN][1000 genomes]
rs907087	0.84[ASN][1000 genomes]
rs907088	0.84[ASN][1000 genomes]
rs907089	0.84[ASN][1000 genomes]
rs907090	0.84[ASN][1000 genomes]
rs907094	0.97[ASN][1000 genomes]
rs9303274	0.85[ASN][1000 genomes]
rs9675194	0.84[ASN][1000 genomes]
rs9915323	0.89[ASN][1000 genomes]
rs9972882	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3794712	PGAP3	cis	Thyroid	GTEx
rs3794712	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37783400-37792200	Weak transcription	Lung	lung
2	chr17:37784600-37792800	Weak transcription	Right Atrium	heart
3	chr17:37785200-37792800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr17:37785200-37792800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:37785400-37792600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:37785800-37792400	Weak transcription	Fetal Lung	lung
7	chr17:37786800-37792000	Weak transcription	Spleen	Spleen
8	chr17:37787000-37792600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr17:37787400-37792800	Enhancers	Fetal Thymus	thymus
10	chr17:37788000-37791800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:37788000-37792600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:37788200-37792400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:37788200-37792600	Enhancers	Brain Substantia Nigra	brain
14	chr17:37788200-37792600	Weak transcription	HMEC	breast
15	chr17:37788200-37793000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:37788200-37793400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:37788400-37791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:37788400-37792600	Weak transcription	NHEK	skin
19	chr17:37788400-37793000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:37788600-37792800	Weak transcription	Fetal Brain Female	brain
21	chr17:37788800-37792200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr17:37788800-37792800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:37789000-37791600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr17:37789000-37792000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:37789200-37792000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:37789400-37791800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr17:37789400-37791800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr17:37789400-37793000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr17:37789600-37792400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr17:37789800-37792600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:37789800-37792600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:37789800-37792600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:37790000-37791600	Enhancers	Duodenum Mucosa	Duodenum
34	chr17:37790000-37792600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr17:37790000-37792600	Genic enhancers	Rectal Mucosa Donor 29	rectum
36	chr17:37790000-37793200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:37790200-37791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:37790200-37792600	Enhancers	Primary B cells from peripheral blood	blood
39	chr17:37790400-37792400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:37790400-37792600	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr17:37790400-37792600	Enhancers	HepG2	liver
42	chr17:37790400-37792800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr17:37790400-37792800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr17:37790400-37792800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr17:37790400-37793400	Weak transcription	Small Intestine	intestine
46	chr17:37790600-37792400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr17:37790600-37792600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr17:37790600-37792600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr17:37790600-37792600	Genic enhancers	Brain Anterior Caudate	brain
50	chr17:37790600-37792600	Enhancers	K562	blood

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