Variant report

Variant	rs385681
Chromosome Location	chr19:39569928-39569929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39568958-39570060	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39568864-39569945	PANC-1	pancreas:	n/a	n/a
3	SIX5	chr19:39568762-39570027	A549	lung:	n/a	n/a
4	SIN3AK20	chr19:39568880-39570038	HCT-116	colon:	n/a	n/a
5	FOSL2	chr19:39569043-39570017	SK-N-SH	brain:	n/a	n/a
6	SP1	chr19:39568936-39569985	HCT-116	colon:	n/a	n/a
7	FOSL1	chr19:39569022-39570045	HCT-116	colon:	n/a	n/a
8	SP1	chr19:39568849-39570080	A549	lung:	n/a	n/a
9	MAX	chr19:39568935-39569944	A549	lung:	n/a	n/a
10	GATA3	chr19:39568837-39569951	A549	lung:	n/a	n/a
11	MAX	chr19:39568904-39570048	HCT-116	colon:	n/a	n/a
12	CBX3	chr19:39568869-39569976	HCT-116	colon:	n/a	n/a
13	MAX	chr19:39568850-39570060	A549	lung:	n/a	n/a
14	RXRA	chr19:39569094-39570030	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr19:39568910-39569930	U87	brain:	n/a	n/a
16	NFIC	chr19:39568895-39569979	SK-N-SH	brain:	n/a	n/a
17	PBX3	chr19:39569053-39569949	A549	lung:	n/a	n/a
18	CEBPB	chr19:39568867-39570119	HCT-116	colon:	n/a	n/a
19	JUND	chr19:39569024-39569944	SK-N-SH	brain:	n/a	n/a
20	JUND	chr19:39568929-39570051	HCT-116	colon:	n/a	n/a
21	EP300	chr19:39568804-39570054	A549	lung:	n/a	n/a
22	EP300	chr19:39568823-39570047	A549	lung:	n/a	n/a
23	NR2F2	chr19:39569303-39569948	MCF-7	breast:	n/a	n/a
24	CEBPB	chr19:39569000-39570126	HCT-116	colon:	n/a	n/a
25	POLR2A	chr19:39568141-39570880	K562	blood:	n/a	n/a
26	JUND	chr19:39568971-39570029	HCT-116	colon:	n/a	n/a
27	JUND	chr19:39568972-39569952	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr19:39568802-39570028	A549	lung:	n/a	n/a
29	TEAD4	chr19:39569036-39569948	A549	lung:	n/a	n/a
30	FOSL2	chr19:39568839-39570074	A549	lung:	n/a	n/a
31	TCF12	chr19:39568841-39569977	SK-N-SH	brain:	n/a	n/a
32	REST	chr19:39568902-39569944	A549	lung:	n/a	n/a
33	POLR2A	chr19:39569016-39569965	U87	brain:	n/a	n/a
34	SP1	chr19:39568887-39570041	A549	lung:	n/a	n/a
35	CEBPB	chr19:39569041-39569986	A549	lung:	n/a	n/a
36	SP1	chr19:39568831-39570126	HCT-116	colon:	n/a	n/a
37	CEBPB	chr19:39569591-39569950	MCF-7	breast:	n/a	n/a
38	EP300	chr19:39568950-39570064	SK-N-SH	brain:	n/a	n/a
39	RCOR1	chr19:39568681-39570127	IMR90	lung:	n/a	n/a
40	ATF3	chr19:39568971-39569949	A549	lung:	n/a	n/a
41	MAX	chr19:39568919-39569985	SK-N-SH	brain:	n/a	n/a
42	CEBPB	chr19:39568911-39570127	A549	lung:	n/a	n/a
43	FOSL1	chr19:39568874-39570136	HCT-116	colon:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000183760	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12151180	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2569365	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34738600	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs377373	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs380679	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs384605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs392005	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs392135	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395387	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs396616	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs397189	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs400011	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420682	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs426076	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs452666	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453853	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802015	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4803196	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs482679	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487456	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs578940	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs597995	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602744	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs609327	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs648635	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs665998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs690812	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691059	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691114	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691256	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691266	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs691391	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs691890	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs692294	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692343	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692347	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs774727	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774927	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39562000-39570000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:39565000-39571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:39565400-39573000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:39565400-39573200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:39567400-39574000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:39568000-39570800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:39568400-39570000	Enhancers	NHDF-Ad	bronchial
8	chr19:39568400-39570000	Enhancers	NHEK	skin
9	chr19:39568400-39570200	Enhancers	Brain Anterior Caudate	brain
10	chr19:39568400-39570600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:39568400-39571600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:39568600-39570200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:39568600-39570200	Enhancers	HMEC	breast
14	chr19:39568800-39570400	Enhancers	Osteobl	bone
15	chr19:39569000-39570200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr19:39569200-39570200	Enhancers	Brain Hippocampus Middle	brain
17	chr19:39569200-39570200	Enhancers	Placenta	Placenta
18	chr19:39569600-39570000	Enhancers	HSMM	muscle
19	chr19:39569600-39570200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:39569600-39570200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:39569800-39570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:39569800-39570800	Enhancers	A549	lung
23	chr19:39569800-39573400	Weak transcription	Brain Substantia Nigra	brain
24	chr19:39569800-39573400	Weak transcription	Hela-S3	cervix
25	chr19:39569800-39573600	Weak transcription	HUVEC	blood vessel
26	chr19:39569800-39573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:39569800-39573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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