Variant report

Variant	rs3813065
Chromosome Location	chr18:39534825-39534826
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	SP1	chr18:39534800-39535356	GM12878	blood:	n/a	chr18:39535150-39535162 chr18:39535150-39535161
2	NRF1	chr18:39534467-39535583	SK-N-SH	brain:	n/a	chr18:39535068-39535079 chr18:39535070-39535079 chr18:39535068-39535082 chr18:39535067-39535078
3	POLR2A	chr18:39534763-39536031	GM12891	blood:	n/a	n/a
4	MAFK	chr18:39534795-39535438	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:39534602-39535714	GM12878	blood:	n/a	n/a
6	IRF1	chr18:39534597-39535456	K562	blood:	n/a	chr18:39534753-39534766 chr18:39534899-39534915 chr18:39535150-39535164 chr18:39534755-39534765
7	ARID3A	chr18:39534615-39535479	K562	blood:	n/a	n/a
8	ZNF384	chr18:39534370-39535447	GM12878	blood:	n/a	n/a
9	MYC	chr18:39534607-39536327	K562	blood:	n/a	chr18:39535370-39535379 chr18:39535066-39535076 chr18:39535767-39535777
10	YY1	chr18:39534739-39535438	H1-hESC	embryonic stem cell:	n/a	chr18:39535148-39535157 chr18:39535376-39535387 chr18:39535038-39535060
11	NRF1	chr18:39534456-39535246	K562	blood:	n/a	chr18:39535068-39535079 chr18:39535070-39535079 chr18:39535068-39535082 chr18:39535067-39535078
12	CTCF	chr18:39534736-39536055	K562	blood:	n/a	n/a
13	BHLHE40	chr18:39534757-39535587	GM12878	blood:	n/a	n/a
14	EGR1	chr18:39534768-39535572	HCT-116	colon:	n/a	chr18:39535146-39535159 chr18:39535146-39535159 chr18:39535146-39535160 chr18:39535149-39535158 chr18:39535353-39535368 chr18:39535147-39535161 chr18:39535146-39535159 chr18:39535146-39535159 chr18:39535145-39535160 chr18:39535149-39535159 chr18:39535373-39535383 chr18:39535147-39535158
15	ZC3H11A	chr18:39534544-39535589	K562	blood:	n/a	n/a
16	ELF1	chr18:39534798-39535371	A549	lung:	n/a	chr18:39535156-39535169 chr18:39535158-39535169 chr18:39535159-39535168
17	EP300	chr18:39534561-39536421	K562	blood:	n/a	chr18:39535342-39535355 chr18:39535161-39535168
18	CREB1	chr18:39534769-39535447	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr18:39534714-39536028	K562	blood:	n/a	n/a
20	ATF2	chr18:39534755-39535211	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr18:39534400-39537224	K562	blood:	n/a	n/a
22	MAZ	chr18:39534817-39535394	Hela-S3	cervix:	n/a	chr18:39535370-39535379
23	MXI1	chr18:39534628-39535979	GM12878	blood:	n/a	n/a
24	ELK1	chr18:39534579-39536143	K562	blood:	n/a	chr18:39535160-39535169 chr18:39535160-39535169
25	MAX	chr18:39534794-39535363	A549	lung:	n/a	chr18:39535066-39535076
26	ELF1	chr18:39534749-39535393	A549	lung:	n/a	chr18:39535156-39535169 chr18:39535158-39535169 chr18:39535159-39535168
27	REST	chr18:39534784-39535766	H1-neurons	neurons:	n/a	n/a
28	SETDB1	chr18:39534727-39535320	U2OS	brain:	n/a	n/a
29	ATF2	chr18:39534811-39535428	GM12878	blood:	n/a	n/a
30	SIX5	chr18:39534815-39535267	A549	lung:	n/a	n/a
31	YY1	chr18:39534806-39535291	HCT-116	colon:	n/a	chr18:39535148-39535157 chr18:39535038-39535060
32	TCF12	chr18:39534694-39535206	A549	lung:	n/a	n/a
33	POLR2A	chr18:39534747-39535631	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr18:39534636-39536081	K562	blood:	n/a	chr18:39535370-39535379 chr18:39535066-39535076 chr18:39535767-39535777
35	THAP1	chr18:39534756-39535283	K562	blood:	n/a	chr18:39535035-39535059
36	CREB1	chr18:39534685-39535594	GM12878	blood:	n/a	n/a
37	TBP	chr18:39534680-39536015	K562	blood:	n/a	n/a
38	FOXA1	chr18:39534795-39535297	HepG2	liver:	n/a	n/a
39	CHD2	chr18:39534651-39535434	GM12878	blood:	n/a	n/a
40	POLR2A	chr18:39534733-39536331	K562	blood:	n/a	n/a
41	YY1	chr18:39534756-39535403	HepG2	liver:	n/a	chr18:39535148-39535157 chr18:39535376-39535387 chr18:39535038-39535060
42	GABPA	chr18:39534754-39535627	SK-N-SH	brain:	n/a	chr18:39535068-39535079 chr18:39535070-39535079 chr18:39535068-39535082
43	RCOR1	chr18:39534563-39535839	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr18:39534709-39535469	GM12878	blood:	n/a	n/a
45	YY1	chr18:39534791-39535288	A549	lung:	n/a	chr18:39535148-39535157 chr18:39535038-39535060
46	NFYB	chr18:39534625-39535399	GM12878	blood:	n/a	n/a
47	GATA1	chr18:39534646-39535768	PBDE	blood:	n/a	n/a
48	IRF1	chr18:39534564-39536718	K562	blood:	n/a	chr18:39534753-39534766 chr18:39535871-39535884 chr18:39534899-39534915 chr18:39535150-39535164 chr18:39534755-39534765
49	CREB1	chr18:39534726-39535500	GM12878	blood:	n/a	n/a
50	YY1	chr18:39534786-39535256	A549	lung:	n/a	chr18:39535148-39535157 chr18:39535038-39535060

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10502776	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11082256	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605021	0.83[ASN][1000 genomes]
rs12606434	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607810	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12953847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954899	0.84[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12956553	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957030	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12962602	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12962732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544260	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16960213	0.84[ASN][1000 genomes]
rs16975459	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975462	0.85[ASN][1000 genomes]
rs28438873	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28541909	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28708684	0.84[ASN][1000 genomes]
rs35269653	0.82[EUR][1000 genomes]
rs35617320	0.81[EUR][1000 genomes]
rs3819162	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4121817	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4513183	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55971157	0.82[ASN][1000 genomes]
rs56680148	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61682064	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62082292	0.82[EUR][1000 genomes]
rs67084667	0.87[AMR][1000 genomes]
rs7230624	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7230883	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs7233661	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7237737	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237780	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237783	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7238178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239652	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240218	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241401	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7242727	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73454598	0.85[ASN][1000 genomes]
rs8087875	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8092954	0.88[EUR][1000 genomes]
rs8095411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646518	0.84[CEU][hapmap]
rs9949409	0.83[ASN][1000 genomes]
rs9949895	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9954624	0.85[ASN][1000 genomes]
rs9956832	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9958749	0.83[ASN][1000 genomes]
rs9964331	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9965466	0.85[ASN][1000 genomes]
rs9966146	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3813065	PIK3C3	cis	parietal	SCAN
rs3813065	PIK3C3	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39524600-39535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:39526600-39535600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:39534400-39535000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr18:39534400-39535000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr18:39534400-39535000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr18:39534400-39535200	Active TSS	HepG2	liver
7	chr18:39534400-39535800	Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr18:39534400-39536200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:39534400-39537000	Active TSS	K562	blood
10	chr18:39534600-39535000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr18:39534600-39535000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr18:39534600-39535000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr18:39534600-39535000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr18:39534600-39535000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr18:39534600-39535000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr18:39534600-39535000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr18:39534600-39535000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr18:39534600-39535000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr18:39534600-39535000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:39534600-39535000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr18:39534600-39535000	Flanking Active TSS	Liver	Liver
22	chr18:39534600-39535000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr18:39534600-39535000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr18:39534600-39535200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:39534600-39535800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:39534600-39535800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:39534600-39535800	Active TSS	Primary T cells fromperipheralblood	blood
28	chr18:39534600-39535800	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr18:39534600-39535800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr18:39534600-39535800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:39534600-39535800	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr18:39534600-39535800	Active TSS	Brain Angular Gyrus	brain
33	chr18:39534600-39535800	Active TSS	Brain Anterior Caudate	brain
34	chr18:39534600-39535800	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr18:39534600-39535800	Active TSS	Brain Substantia Nigra	brain
36	chr18:39534600-39535800	Active TSS	Duodenum Mucosa	Duodenum
37	chr18:39534600-39535800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr18:39534600-39535800	Active TSS	Fetal Brain Male	brain
39	chr18:39534600-39535800	Active TSS	Fetal Brain Female	brain
40	chr18:39534600-39535800	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr18:39534600-39535800	Active TSS	Rectal Smooth Muscle	rectum
42	chr18:39534600-39535800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr18:39534600-39535800	Active TSS	Stomach Mucosa	stomach
44	chr18:39534600-39535800	Active TSS	Thymus	Thymus
45	chr18:39534600-39535800	Active TSS	Osteobl	bone
46	chr18:39534600-39536000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr18:39534600-39536000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr18:39534600-39536000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr18:39534600-39536000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr18:39534600-39536000	Active TSS	Brain Cingulate Gyrus	brain

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