Variant report

Variant	rs73454596
Chromosome Location	chr18:39537040-39537041
allele	A/C
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	TBL1XR1	chr18:39534400-39537224	K562	blood:	n/a	n/a
2	GTF2F1	chr18:39536976-39537251	K562	blood:	n/a	n/a
3	POLR2A	chr18:39536868-39537286	GM12878	blood:	n/a	n/a
4	POLR2A	chr18:39534595-39539390	K562	blood:	n/a	n/a
5	CUX1	chr18:39536993-39537341	K562	blood:	n/a	n/a
6	POLR2A	chr18:39536309-39537341	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr18:39536838-39537293	MCF10A-Er-Src	breast:	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]
rs73454593	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39534600-39537200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr18:39534600-39537400	Active TSS	GM12878-XiMat	blood
3	chr18:39535800-39537400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr18:39535800-39537400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr18:39536000-39537200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr18:39536000-39537400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr18:39536000-39537800	Weak transcription	Placenta	Placenta
8	chr18:39536000-39538200	Weak transcription	Gastric	stomach
9	chr18:39536000-39541600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:39536000-39545400	Weak transcription	Lung	lung
11	chr18:39536000-39547000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:39536000-39547000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:39536000-39547000	Weak transcription	Left Ventricle	heart
14	chr18:39536000-39547200	Weak transcription	Esophagus	oesophagus
15	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
16	chr18:39536200-39537200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr18:39536200-39537400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:39536200-39537600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr18:39536200-39537800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr18:39536200-39538000	Weak transcription	Fetal Muscle Leg	muscle
21	chr18:39536200-39538200	Weak transcription	Fetal Thymus	thymus
22	chr18:39536200-39538400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr18:39536200-39542600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr18:39536200-39547000	Weak transcription	Right Ventricle	heart
25	chr18:39536200-39547000	Weak transcription	Thymus	Thymus
26	chr18:39536200-39548000	Weak transcription	Colonic Mucosa	Colon
27	chr18:39536200-39552400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr18:39536200-39564800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr18:39536200-39568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr18:39536400-39537400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr18:39536400-39537400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr18:39536400-39537400	Enhancers	Colon Smooth Muscle	Colon
33	chr18:39536400-39537400	Weak transcription	Fetal Intestine Small	intestine
34	chr18:39536400-39537600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr18:39536400-39537600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr18:39536400-39537800	Enhancers	Adipose Nuclei	Adipose
37	chr18:39536400-39537800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:39536400-39538200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:39536400-39538200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr18:39536400-39538400	Enhancers	Brain Hippocampus Middle	brain
41	chr18:39536400-39540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:39536400-39552400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr18:39536400-39578200	Weak transcription	A549	lung
44	chr18:39536600-39537400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr18:39536600-39537600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr18:39536600-39537600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:39536600-39537600	Enhancers	Primary T cells from cord blood	blood
48	chr18:39536600-39537600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr18:39536600-39538200	Weak transcription	HUVEC	blood vessel
50	chr18:39536800-39537200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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