Variant report

Variant	rs73454598
Chromosome Location	chr18:39537513-39537514
allele	A/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	chr18:39537241-39537969	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:39534595-39539390	K562	blood:	n/a	n/a
3	POLR2A	chr18:39537502-39537734	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10502776	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11082256	0.84[ASN][1000 genomes]
rs12605021	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12606434	0.84[ASN][1000 genomes]
rs12607810	0.85[ASN][1000 genomes]
rs12953847	0.85[ASN][1000 genomes]
rs12956553	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12957030	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12961563	0.85[ASN][1000 genomes]
rs12962602	0.83[ASN][1000 genomes]
rs12962732	0.85[ASN][1000 genomes]
rs1544260	0.82[ASN][1000 genomes]
rs16960213	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16975459	0.85[ASN][1000 genomes]
rs16975462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438873	0.81[ASN][1000 genomes]
rs28541909	0.81[ASN][1000 genomes]
rs28708684	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3813065	0.85[ASN][1000 genomes]
rs3819162	0.84[ASN][1000 genomes]
rs4121817	0.84[ASN][1000 genomes]
rs4513183	0.82[ASN][1000 genomes]
rs55971157	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs56680148	0.84[ASN][1000 genomes]
rs7230624	0.80[ASN][1000 genomes]
rs7233661	0.84[ASN][1000 genomes]
rs7237737	0.81[ASN][1000 genomes]
rs7237780	0.81[ASN][1000 genomes]
rs7237783	0.83[ASN][1000 genomes]
rs7238178	0.82[ASN][1000 genomes]
rs7239652	0.82[ASN][1000 genomes]
rs7240218	0.82[ASN][1000 genomes]
rs7242727	0.84[ASN][1000 genomes]
rs8087875	0.82[ASN][1000 genomes]
rs8095411	0.83[ASN][1000 genomes]
rs9949409	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9949895	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9954624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9956832	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9958749	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9964331	0.84[ASN][1000 genomes]
rs9965466	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966146	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39537800	Weak transcription	Placenta	Placenta
2	chr18:39536000-39538200	Weak transcription	Gastric	stomach
3	chr18:39536000-39541600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:39536000-39545400	Weak transcription	Lung	lung
5	chr18:39536000-39547000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:39536000-39547000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:39536000-39547000	Weak transcription	Left Ventricle	heart
8	chr18:39536000-39547200	Weak transcription	Esophagus	oesophagus
9	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
10	chr18:39536200-39537600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr18:39536200-39537800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:39536200-39538000	Weak transcription	Fetal Muscle Leg	muscle
13	chr18:39536200-39538200	Weak transcription	Fetal Thymus	thymus
14	chr18:39536200-39538400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr18:39536200-39542600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr18:39536200-39547000	Weak transcription	Right Ventricle	heart
17	chr18:39536200-39547000	Weak transcription	Thymus	Thymus
18	chr18:39536200-39548000	Weak transcription	Colonic Mucosa	Colon
19	chr18:39536200-39552400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr18:39536200-39564800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:39536200-39568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:39536400-39537600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr18:39536400-39537600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr18:39536400-39537800	Enhancers	Adipose Nuclei	Adipose
25	chr18:39536400-39537800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:39536400-39538200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr18:39536400-39538200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr18:39536400-39538400	Enhancers	Brain Hippocampus Middle	brain
29	chr18:39536400-39540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:39536400-39552400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:39536400-39578200	Weak transcription	A549	lung
32	chr18:39536600-39537600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:39536600-39537600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:39536600-39537600	Enhancers	Primary T cells from cord blood	blood
35	chr18:39536600-39537600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr18:39536600-39538200	Weak transcription	HUVEC	blood vessel
37	chr18:39536800-39537600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:39536800-39537600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr18:39536800-39537600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr18:39536800-39537600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:39536800-39537600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr18:39536800-39537600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:39536800-39537600	Enhancers	Liver	Liver
44	chr18:39536800-39537600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr18:39536800-39537600	Weak transcription	Fetal Intestine Large	intestine
46	chr18:39536800-39537600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr18:39536800-39537600	Enhancers	Rectal Smooth Muscle	rectum
48	chr18:39536800-39537600	Weak transcription	Small Intestine	intestine
49	chr18:39536800-39537600	Weak transcription	NHLF	lung
50	chr18:39536800-39537800	Enhancers	Brain Angular Gyrus	brain

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