Variant report

Variant	rs73452300
Chromosome Location	chr18:39611098-39611099
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	chr18:39609953-39611131	SK-N-SH	brain:	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]
rs11872115	0.81[AFR][1000 genomes]
rs11873469	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873602	1.00[EUR][1000 genomes]
rs11874766	1.00[EUR][1000 genomes]
rs11874775	1.00[EUR][1000 genomes]
rs11874814	1.00[EUR][1000 genomes]
rs11874830	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876547	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876578	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11877901	1.00[EUR][1000 genomes]
rs1540057	1.00[EUR][1000 genomes]
rs16975441	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975447	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975463	1.00[EUR][1000 genomes]
rs16975466	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975521	0.81[AFR][1000 genomes];0.87[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	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56751463	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56979511	1.00[EUR][1000 genomes]
rs57208863	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575366	1.00[EUR][1000 genomes]
rs58298297	0.81[AFR][1000 genomes];0.87[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	0.87[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]
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	1.00[EUR][1000 genomes]
rs6507454	1.00[EUR][1000 genomes]
rs655693	1.00[EUR][1000 genomes]
rs659950	1.00[EUR][1000 genomes]
rs6650669	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	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237185	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237815	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7239880	1.00[EUR][1000 genomes]
rs7240066	1.00[EUR][1000 genomes]
rs7241399	1.00[EUR][1000 genomes]
rs7242077	1.00[EUR][1000 genomes]
rs7245131	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7343027	1.00[EUR][1000 genomes]
rs73448558	1.00[EUR][1000 genomes]
rs73451096	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73453013	1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454580	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454581	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454593	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454596	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454602	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73950814	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8084037	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8085708	1.00[EUR][1000 genomes]
rs8088187	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8089142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8090403	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8095945	0.87[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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
5	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
6	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
7	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:39584600-39618600	Weak transcription	NHLF	lung
9	chr18:39585000-39611400	Weak transcription	Gastric	stomach
10	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
11	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
12	chr18:39585200-39612000	Weak transcription	NHEK	skin
13	chr18:39585400-39627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:39585600-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr18:39586400-39613000	Weak transcription	Brain Substantia Nigra	brain
16	chr18:39586400-39619000	Weak transcription	HUVEC	blood vessel
17	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
18	chr18:39587000-39619400	Weak transcription	Lung	lung
19	chr18:39587200-39611400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:39587200-39614200	Weak transcription	Ovary	ovary
21	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
22	chr18:39592200-39629400	Weak transcription	Fetal Brain Female	brain
23	chr18:39594000-39614400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr18:39594600-39638800	Weak transcription	K562	blood
25	chr18:39596200-39618800	Weak transcription	Brain Germinal Matrix	brain
26	chr18:39597400-39622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
28	chr18:39601600-39611400	Weak transcription	Left Ventricle	heart
29	chr18:39601600-39612800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr18:39601600-39612800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:39601800-39612800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr18:39602000-39613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr18:39602200-39614200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr18:39602200-39614200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:39602200-39617200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr18:39602200-39620800	Weak transcription	A549	lung
38	chr18:39604800-39613800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr18:39605000-39612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:39605600-39619000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr18:39605600-39620400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:39606200-39614400	Weak transcription	Primary B cells from cord blood	blood
43	chr18:39606200-39618400	Weak transcription	HepG2	liver
44	chr18:39606200-39628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr18:39606800-39611600	Weak transcription	Fetal Lung	lung
46	chr18:39607400-39626000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr18:39607600-39634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr18:39608600-39627400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr18:39608800-39631400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr18:39609000-39613800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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