Variant report

Variant	rs907094
Chromosome Location	chr17:37790371-37790372
allele	C/T
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	CTCF	chr17:37790366-37791140	K562	blood:	n/a	chr17:37790836-37790852 chr17:37790835-37790853 chr17:37790840-37790848 chr17:37790830-37790851
2	CTCF	chr17:37789741-37791243	A549	lung:	n/a	chr17:37790836-37790852 chr17:37790835-37790853 chr17:37790840-37790848 chr17:37790830-37790851
3	CTCF	chr17:37790322-37791165	HCT-116	colon:	n/a	chr17:37790836-37790852 chr17:37790835-37790853 chr17:37790840-37790848 chr17:37790830-37790851
4	CTCF	chr17:37790222-37791292	HCT-116	colon:	n/a	chr17:37790836-37790852 chr17:37790835-37790853 chr17:37790840-37790848 chr17:37790830-37790851
5	POLR2A	chr17:37790252-37790717	HepG2	liver:	n/a	n/a
6	CTCF	chr17:37790058-37791257	SK-N-SH	brain:	n/a	chr17:37790836-37790852 chr17:37790835-37790853 chr17:37790840-37790848 chr17:37790830-37790851
7	CTCF	chr17:37790280-37790430	WI-38	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37790354..37790890-chr17:37910125..37910633,2	K562	blood:
2	chr17:37776436..37778537-chr17:37788682..37790894,2	MCF-7	breast:
3	chr17:37782244..37782963-chr17:37790351..37790853,2	K562	blood:
4	chr17:37790210..37790930-chr17:37828221..37828992,2	MCF-7	breast:
5	chr17:37785506..37788397-chr17:37788916..37793369,4	K562	blood:
6	chr17:37788816..37790595-chr17:38326120..38328082,2	K562	blood:
7	chr17:37789471..37791960-chr17:37905766..37908053,2	MCF-7	breast:
8	chr17:37789952..37790826-chr17:37809840..37810573,2	K562	blood:
9	chr17:37789742..37792172-chr17:37795424..37797567,2	MCF-7	breast:
10	chr17:37789315..37792571-chr17:37910228..37913282,4	K562	blood:

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

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1018246	0.87[ASN][1000 genomes]
rs1053651	0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs10852934	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11651497	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658786	0.89[ASN][1000 genomes]
rs11869286	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12150047	0.83[CEU][hapmap]
rs12150298	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12150603	0.82[ASW][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12453682	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.90[ASN][1000 genomes]
rs12940986	0.82[ASW][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs14050	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1476278	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1495099	0.99[ASN][1000 genomes]
rs1495100	0.87[ASN][1000 genomes]
rs1495101	0.87[ASN][1000 genomes]
rs1495102	0.87[ASN][1000 genomes]
rs1565920	0.87[ASN][1000 genomes]
rs1565922	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1874228	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];0.97[ASN][1000 genomes]
rs1877031	0.88[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];0.91[ASN][1000 genomes]
rs2247862	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271308	0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2271309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2313171	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2517952	0.80[ASN][1000 genomes]
rs2517953	0.82[ASN][1000 genomes]
rs2517954	0.81[ASN][1000 genomes]
rs2517955	0.82[ASW][hapmap];0.80[ASN][1000 genomes]
rs2517956	0.80[ASN][1000 genomes]
rs2517957	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2517958	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2517959	0.81[ASN][1000 genomes]
rs2934951	0.87[ASN][1000 genomes]
rs2934952	0.87[ASN][1000 genomes]
rs2934953	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2934956	0.87[ASN][1000 genomes]
rs2941503	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2941504	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2941505	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2941506	0.87[ASN][1000 genomes]
rs2952151	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2952152	0.86[ASN][1000 genomes]
rs33953566	0.99[ASN][1000 genomes]
rs3751903	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794712	0.97[ASN][1000 genomes]
rs3817160	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs407307	0.84[ASN][1000 genomes]
rs4794817	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795388	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4795389	0.97[ASN][1000 genomes]
rs4795390	0.99[ASN][1000 genomes]
rs732083	0.87[ASN][1000 genomes]
rs732084	0.87[ASN][1000 genomes]
rs8077172	0.87[ASN][1000 genomes]
rs8078228	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs879606	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs881844	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs903501	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs903502	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907087	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907088	0.87[ASN][1000 genomes]
rs907089	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907090	0.87[ASN][1000 genomes]
rs9303274	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs931992	0.88[ASW][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap]
rs9675194	0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9915323	0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs9972882	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.91[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs907094	SPACA3	cis	parietal	SCAN
rs907094	SLFN14	cis	parietal	SCAN
rs907094	IGFBP4	cis	parietal	SCAN
rs907094	DHRS11	cis	cerebellum	SCAN
rs907094	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs907094	PGAP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37778800-37790600	Weak transcription	K562	blood
2	chr17:37783400-37792200	Weak transcription	Lung	lung
3	chr17:37783600-37790600	Weak transcription	Gastric	stomach
4	chr17:37784600-37792800	Weak transcription	Right Atrium	heart
5	chr17:37785000-37791000	Weak transcription	Esophagus	oesophagus
6	chr17:37785200-37792800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr17:37785200-37792800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:37785400-37792600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:37785800-37792400	Weak transcription	Fetal Lung	lung
10	chr17:37786600-37791400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:37786800-37792000	Weak transcription	Spleen	Spleen
12	chr17:37787000-37790400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:37787000-37792600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr17:37787400-37791200	Enhancers	Fetal Intestine Large	intestine
15	chr17:37787400-37792800	Enhancers	Fetal Thymus	thymus
16	chr17:37787600-37791200	Enhancers	Stomach Mucosa	stomach
17	chr17:37787800-37791200	Enhancers	Brain Angular Gyrus	brain
18	chr17:37787800-37791200	Enhancers	Brain Hippocampus Middle	brain
19	chr17:37788000-37790600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:37788000-37791800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:37788000-37792600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:37788200-37790400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:37788200-37790600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr17:37788200-37790600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:37788200-37791000	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:37788200-37791200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr17:37788200-37792400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:37788200-37792600	Enhancers	Brain Substantia Nigra	brain
29	chr17:37788200-37792600	Weak transcription	HMEC	breast
30	chr17:37788200-37793000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:37788200-37793400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr17:37788400-37790400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr17:37788400-37790600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr17:37788400-37790800	Weak transcription	Fetal Kidney	kidney
35	chr17:37788400-37791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:37788400-37792600	Weak transcription	NHEK	skin
37	chr17:37788400-37793000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:37788600-37792800	Weak transcription	Fetal Brain Female	brain
39	chr17:37788800-37790600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr17:37788800-37791000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:37788800-37791200	Enhancers	Adipose Nuclei	Adipose
42	chr17:37788800-37792200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:37788800-37792800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:37789000-37790400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:37789000-37790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr17:37789000-37790600	Weak transcription	Primary T cells from cord blood	blood
47	chr17:37789000-37790600	Weak transcription	Fetal Brain Male	brain
48	chr17:37789000-37791000	Weak transcription	A549	lung
49	chr17:37789000-37791200	Enhancers	Pancreas	Pancrea
50	chr17:37789000-37791600	Weak transcription	H9 Cell Line	embryonic stem cell

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