Variant report

Variant	rs28419351
Chromosome Location	chr14:39903205-39903206
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	MBD4	chr14:39901240-39903267	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:39900018-39903209	GM12891	blood:	n/a	n/a
3	POLR2A	chr14:39900584-39903973	MCF10A-Er-Src	breast:	n/a	n/a
4	SREBP1	chr14:39901045-39904492	GM12878	blood:	n/a	chr14:39901741-39901751 chr14:39903823-39903837

No.	Distal block	Cell Line	Cell type
1	chr14:39638023..39641762-chr14:39900094..39905872,5	MCF-7	breast:
2	chr14:39903003..39906043-chr14:39907787..39910140,3	MCF-7	breast:
3	chr14:39572264..39573816-chr14:39900834..39903460,2	MCF-7	breast:

Variant related genes	Relation type
FBXO33	TF binding region
ENSG00000258651	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10047876	0.90[ASN][1000 genomes]
rs10130181	0.85[ASN][1000 genomes]
rs10132190	0.85[ASN][1000 genomes]
rs10133746	0.88[ASN][1000 genomes]
rs10134065	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10136490	0.90[ASN][1000 genomes]
rs10136915	0.90[ASN][1000 genomes]
rs10142029	0.90[ASN][1000 genomes]
rs10143148	0.88[ASN][1000 genomes]
rs10144377	0.85[ASN][1000 genomes]
rs10145757	0.85[ASN][1000 genomes]
rs10146106	0.90[ASN][1000 genomes]
rs10146622	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10483538	0.81[ASN][1000 genomes]
rs12185014	0.88[ASN][1000 genomes]
rs12431558	0.81[ASN][1000 genomes]
rs12433987	0.85[ASN][1000 genomes]
rs17109168	0.90[ASN][1000 genomes]
rs17622868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103795	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179973	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28398804	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454173	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568594	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571663	0.85[ASN][1000 genomes]
rs28704775	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28871954	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899887	0.85[ASN][1000 genomes]
rs4316662	0.85[ASN][1000 genomes]
rs4902559	0.85[ASN][1000 genomes]
rs61999073	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61999077	1.00[ASN][1000 genomes]
rs61999079	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000696	0.85[ASN][1000 genomes]
rs62000708	0.85[ASN][1000 genomes]
rs62000709	0.85[ASN][1000 genomes]
rs62000710	0.85[ASN][1000 genomes]
rs62000711	0.81[ASN][1000 genomes]
rs62000715	0.83[ASN][1000 genomes]
rs62000720	0.82[ASN][1000 genomes]
rs62001106	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62015674	0.90[ASN][1000 genomes]
rs62015677	0.90[ASN][1000 genomes]
rs7146753	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156962	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158282	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161482	0.90[ASN][1000 genomes]
rs8006076	0.90[ASN][1000 genomes]
rs8007036	0.90[ASN][1000 genomes]
rs9322999	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9805937	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39899800-39903400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr14:39902400-39910200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:39902400-39911400	Weak transcription	Gastric	stomach
4	chr14:39902800-39903400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr14:39902800-39903400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr14:39902800-39903400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr14:39902800-39903400	Flanking Active TSS	GM12878-XiMat	blood
8	chr14:39902800-39910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:39903000-39903400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr14:39903000-39903400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:39903000-39910000	Weak transcription	Lung	lung
12	chr14:39903000-39910800	Weak transcription	Fetal Brain Male	brain
13	chr14:39903000-39911200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:39903000-39912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:39903000-39916400	Weak transcription	Fetal Heart	heart
16	chr14:39903200-39903400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:39903200-39903400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:39903200-39903400	Enhancers	Liver	Liver
19	chr14:39903200-39903400	Enhancers	A549	lung
20	chr14:39903200-39903400	Flanking Active TSS	Hela-S3	cervix
21	chr14:39903200-39903400	Flanking Active TSS	HepG2	liver
22	chr14:39903200-39903400	Active TSS	HMEC	breast
23	chr14:39903200-39903400	Enhancers	Osteobl	bone
24	chr14:39903200-39904000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:39903200-39904000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr14:39903200-39904400	Weak transcription	Brain Anterior Caudate	brain
27	chr14:39903200-39910800	Weak transcription	Brain Hippocampus Middle	brain
28	chr14:39903200-39912000	Weak transcription	Aorta	Aorta

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