Variant report

Variant	rs73454593
Chromosome Location	chr18:39535420-39535421
allele	C/G
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	POLR2A	chr18:39535037-39535495	ProgFib	skin:	n/a	n/a
2	POLR2A	chr18:39535007-39535547	GM12891	blood:	n/a	n/a
3	NFYA	chr18:39534850-39535471	K562	blood:	n/a	n/a
4	NRF1	chr18:39534467-39535583	SK-N-SH	brain:	n/a	chr18:39535068-39535079 chr18:39535070-39535079 chr18:39535068-39535082 chr18:39535067-39535078
5	POLR2A	chr18:39534763-39536031	GM12891	blood:	n/a	n/a
6	MAFK	chr18:39534795-39535438	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr18:39534602-39535714	GM12878	blood:	n/a	n/a
8	ZBTB7A	chr18:39535295-39535463	K562	blood:	n/a	n/a
9	IRF1	chr18:39534597-39535456	K562	blood:	n/a	chr18:39534753-39534766 chr18:39534899-39534915 chr18:39535150-39535164 chr18:39534755-39534765
10	POLR2A	chr18:39534960-39535594	K562	blood:	n/a	n/a
11	ARID3A	chr18:39534615-39535479	K562	blood:	n/a	n/a
12	POLR2A	chr18:39534865-39536449	PBDE	blood:	n/a	n/a
13	POLR2A	chr18:39534973-39535568	Raji	blood:	n/a	n/a
14	TCF7L2	chr18:39535001-39535552	Hela-S3	cervix:	n/a	n/a
15	SIN3A	chr18:39534897-39535539	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF384	chr18:39534370-39535447	GM12878	blood:	n/a	n/a
17	MYC	chr18:39534607-39536327	K562	blood:	n/a	chr18:39535370-39535379 chr18:39535066-39535076 chr18:39535767-39535777
18	RUNX3	chr18:39535078-39535457	GM12878	blood:	n/a	n/a
19	POLR2A	chr18:39535014-39535613	GM12878	blood:	n/a	n/a
20	POLR2A	chr18:39534921-39535449	HUVEC	blood vessel:	n/a	n/a
21	YY1	chr18:39534739-39535438	H1-hESC	embryonic stem cell:	n/a	chr18:39535148-39535157 chr18:39535376-39535387 chr18:39535038-39535060
22	CTCF	chr18:39535240-39535510	AG04449	skin:	n/a	n/a
23	CTCF	chr18:39534736-39536055	K562	blood:	n/a	n/a
24	BHLHE40	chr18:39534757-39535587	GM12878	blood:	n/a	n/a
25	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
26	ZC3H11A	chr18:39534544-39535589	K562	blood:	n/a	n/a
27	MYC	chr18:39534833-39536229	MCF10A-Er-Src	breast:	n/a	chr18:39535370-39535379 chr18:39535066-39535076 chr18:39535767-39535777
28	EP300	chr18:39534561-39536421	K562	blood:	n/a	chr18:39535342-39535355 chr18:39535161-39535168
29	CREB1	chr18:39534769-39535447	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr18:39534944-39535495	GM18951	blood:	n/a	n/a
31	ZNF143	chr18:39534714-39536028	K562	blood:	n/a	n/a
32	TBL1XR1	chr18:39534400-39537224	K562	blood:	n/a	n/a
33	MXI1	chr18:39534628-39535979	GM12878	blood:	n/a	n/a
34	ELK1	chr18:39534579-39536143	K562	blood:	n/a	chr18:39535160-39535169 chr18:39535160-39535169
35	POLR2A	chr18:39535057-39535469	SK-N-MC	brain:	n/a	n/a
36	REST	chr18:39534784-39535766	H1-neurons	neurons:	n/a	n/a
37	SIN3AK20	chr18:39535095-39535445	H1-hESC	embryonic stem cell:	n/a	n/a
38	BACH1	chr18:39535278-39535887	K562	blood:	n/a	n/a
39	ATF2	chr18:39534811-39535428	GM12878	blood:	n/a	n/a
40	TAF1	chr18:39535010-39535441	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr18:39534981-39535598	K562	blood:	n/a	n/a
42	ELF1	chr18:39534869-39535444	HepG2	liver:	n/a	chr18:39535156-39535169 chr18:39535158-39535169 chr18:39535159-39535168
43	POLR2A	chr18:39535175-39535447	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr18:39535100-39535445	K562	blood:	n/a	n/a
45	POLR2A	chr18:39535019-39535561	HL-60	blood:	n/a	n/a
46	POLR2A	chr18:39534844-39535526	HepG2	liver:	n/a	n/a
47	POLR2A	chr18:39534747-39535631	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chr18:39534636-39536081	K562	blood:	n/a	chr18:39535370-39535379 chr18:39535066-39535076 chr18:39535767-39535777
49	CREB1	chr18:39534685-39535594	GM12878	blood:	n/a	n/a
50	TBP	chr18:39534680-39536015	K562	blood:	n/a	n/a

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1142044	1.00[EUR][1000 genomes]
rs11873469	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873602	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874766	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874775	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874814	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11877901	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1540057	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975441	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975447	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975463	1.00[EUR][1000 genomes]
rs16975466	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2469471	1.00[EUR][1000 genomes]
rs490578	1.00[EUR][1000 genomes]
rs493100	1.00[EUR][1000 genomes]
rs525369	1.00[EUR][1000 genomes]
rs542870	1.00[EUR][1000 genomes]
rs55655849	1.00[EUR][1000 genomes]
rs563840	1.00[EUR][1000 genomes]
rs56411890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56751463	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56979511	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57208863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575366	1.00[EUR][1000 genomes]
rs58298297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs583163	1.00[EUR][1000 genomes]
rs58390786	1.00[EUR][1000 genomes]
rs584022	1.00[EUR][1000 genomes]
rs586797	1.00[EUR][1000 genomes]
rs58881642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs591870	1.00[EUR][1000 genomes]
rs593689	1.00[EUR][1000 genomes]
rs606366	1.00[EUR][1000 genomes]
rs608428	1.00[EUR][1000 genomes]
rs61095714	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs616575	1.00[EUR][1000 genomes]
rs633541	1.00[EUR][1000 genomes]
rs635560	1.00[EUR][1000 genomes]
rs640064	1.00[EUR][1000 genomes]
rs640460	1.00[EUR][1000 genomes]
rs643772	1.00[EUR][1000 genomes]
rs645148	1.00[EUR][1000 genomes]
rs647084	1.00[EUR][1000 genomes]
rs6507453	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6507454	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs655693	1.00[EUR][1000 genomes]
rs659950	1.00[EUR][1000 genomes]
rs6650669	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs669235	1.00[EUR][1000 genomes]
rs670429	1.00[EUR][1000 genomes]
rs674380	1.00[EUR][1000 genomes]
rs684091	1.00[EUR][1000 genomes]
rs7229485	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237185	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7239880	1.00[EUR][1000 genomes]
rs7240066	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7241399	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7242077	1.00[EUR][1000 genomes]
rs7245131	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7343027	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73448558	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73451096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73452300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73453013	1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454580	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454581	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73950814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8084037	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8085708	1.00[EUR][1000 genomes]
rs8088187	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8089142	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8090403	1.00[EUR][1000 genomes]
rs8095945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9948650	1.00[EUR][1000 genomes]
rs9965647	1.00[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39526600-39535600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:39534400-39535800	Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr18:39534400-39536200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr18:39534400-39537000	Active TSS	K562	blood
5	chr18:39534600-39535800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:39534600-39535800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:39534600-39535800	Active TSS	Primary T cells fromperipheralblood	blood
8	chr18:39534600-39535800	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr18:39534600-39535800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:39534600-39535800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr18:39534600-39535800	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr18:39534600-39535800	Active TSS	Brain Angular Gyrus	brain
13	chr18:39534600-39535800	Active TSS	Brain Anterior Caudate	brain
14	chr18:39534600-39535800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr18:39534600-39535800	Active TSS	Brain Substantia Nigra	brain
16	chr18:39534600-39535800	Active TSS	Duodenum Mucosa	Duodenum
17	chr18:39534600-39535800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr18:39534600-39535800	Active TSS	Fetal Brain Male	brain
19	chr18:39534600-39535800	Active TSS	Fetal Brain Female	brain
20	chr18:39534600-39535800	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr18:39534600-39535800	Active TSS	Rectal Smooth Muscle	rectum
22	chr18:39534600-39535800	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr18:39534600-39535800	Active TSS	Stomach Mucosa	stomach
24	chr18:39534600-39535800	Active TSS	Thymus	Thymus
25	chr18:39534600-39535800	Active TSS	Osteobl	bone
26	chr18:39534600-39536000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr18:39534600-39536000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr18:39534600-39536000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:39534600-39536000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:39534600-39536000	Active TSS	Brain Cingulate Gyrus	brain
31	chr18:39534600-39536000	Active TSS	Brain Hippocampus Middle	brain
32	chr18:39534600-39536000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr18:39534600-39536000	Active TSS	NHEK	skin
34	chr18:39534600-39536000	Active TSS	NHLF	lung
35	chr18:39534600-39536200	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr18:39534600-39536200	Active TSS	Fetal Intestine Large	intestine
37	chr18:39534600-39536200	Active TSS	Fetal Intestine Small	intestine
38	chr18:39534600-39536200	Active TSS	Fetal Kidney	kidney
39	chr18:39534600-39536200	Active TSS	Fetal Muscle Leg	muscle
40	chr18:39534600-39536200	Active TSS	Right Ventricle	heart
41	chr18:39534600-39536400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr18:39534600-39536400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr18:39534600-39536400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:39534600-39536400	Active TSS	Stomach Smooth Muscle	stomach
45	chr18:39534600-39536600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr18:39534600-39536600	Active TSS	Ovary	ovary
47	chr18:39534600-39536600	Active TSS	Psoas Muscle	Psoas
48	chr18:39534600-39536600	Active TSS	Hela-S3	cervix
49	chr18:39534600-39536800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr18:39534600-39536800	Active TSS	Aorta	Aorta

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