Variant report

Variant	rs28398804
Chromosome Location	chr14:39902852-39902853
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	MBD4	chr14:39901240-39903267	HepG2	liver:	n/a	n/a
2	FOXA2	chr14:39901178-39902986	HepG2	liver:	n/a	n/a
3	MYBL2	chr14:39901117-39903114	HepG2	liver:	n/a	n/a
4	ARID3A	chr14:39901350-39903055	HepG2	liver:	n/a	n/a
5	MXI1	chr14:39902800-39902998	Hela-S3	cervix:	n/a	n/a
6	HDAC2	chr14:39900390-39902978	HepG2	liver:	n/a	chr14:39902402-39902416 chr14:39902667-39902681 chr14:39902395-39902409 chr14:39902398-39902412 chr14:39902403-39902417 chr14:39902399-39902413 chr14:39902666-39902680 chr14:39902400-39902414
7	CHD1	chr14:39900053-39903161	IMR90	lung:	n/a	n/a
8	POLR2A	chr14:39900402-39903174	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:39899889-39903076	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr14:39900018-39903209	GM12891	blood:	n/a	n/a
11	POLR2A	chr14:39900584-39903973	MCF10A-Er-Src	breast:	n/a	n/a
12	BRCA1	chr14:39901322-39902981	Hela-S3	cervix:	n/a	n/a
13	MYBL2	chr14:39899907-39902913	HepG2	liver:	n/a	n/a
14	SREBP1	chr14:39901045-39904492	GM12878	blood:	n/a	chr14:39901741-39901751 chr14:39903823-39903837
15	POLR2A	chr14:39900671-39903097	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr14:39901797-39903066	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39638023..39641762-chr14:39900094..39905872,5	MCF-7	breast:
2	chr14:39572117..39574614-chr14:39901062..39903055,2	MCF-7	breast:
3	chr14:39902105..39903035-chr20:442777..443759,2	Hela-S3	cervix:
4	chr14:39572264..39573816-chr14:39900834..39903460,2	MCF-7	breast:

Variant related genes	Relation type
FBXO33	TF binding region
ENSG00000258651	Chromatin interaction
ENSG00000125875	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

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	0.95[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]
rs17109185	0.87[AFR][1000 genomes]
rs17109219	0.85[AFR][1000 genomes]
rs17622868	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103795	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179973	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419351	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454173	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568594	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571663	0.85[ASN][1000 genomes]
rs28704775	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28871954	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]
rs56804791	0.87[AFR][1000 genomes]
rs59337169	0.84[AFR][1000 genomes]
rs61999073	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61999077	1.00[ASN][1000 genomes]
rs61999079	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	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62015674	0.90[ASN][1000 genomes]
rs62015677	0.90[ASN][1000 genomes]
rs7140854	0.86[AFR][1000 genomes]
rs7146753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156962	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7158282	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161482	0.90[ASN][1000 genomes]
rs73285548	0.87[AFR][1000 genomes]
rs73285551	0.87[AFR][1000 genomes]
rs73285587	0.87[AFR][1000 genomes]
rs73285597	0.86[AFR][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:6 , 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
6	esv3428481	chr14:39900201-39903099	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 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	chr14:39897800-39903000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr14:39899000-39903000	Active TSS	Psoas Muscle	Psoas
3	chr14:39899000-39903000	Active TSS	Right Atrium	heart
4	chr14:39899000-39903200	Active TSS	Aorta	Aorta
5	chr14:39899000-39903200	Active TSS	Ovary	ovary
6	chr14:39899200-39903000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:39899200-39903200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr14:39899200-39903200	Active TSS	NHLF	lung
9	chr14:39899400-39903000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:39899400-39903200	Active TSS	Right Ventricle	heart
11	chr14:39899600-39903000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:39899600-39903000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:39899600-39903000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:39899600-39903000	Active TSS	Left Ventricle	heart
15	chr14:39899800-39903000	Active TSS	HSMMtube	muscle
16	chr14:39899800-39903200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr14:39899800-39903200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr14:39899800-39903200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:39899800-39903200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:39899800-39903200	Active TSS	Stomach Mucosa	stomach
21	chr14:39899800-39903200	Active TSS	HSMM	muscle
22	chr14:39899800-39903400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr14:39900000-39903000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr14:39900000-39903200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr14:39900000-39903200	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr14:39900000-39903200	Active TSS	Fetal Stomach	stomach
27	chr14:39900200-39903000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:39900200-39903000	Active TSS	Fetal Intestine Large	intestine
29	chr14:39900200-39903000	Active TSS	Lung	lung
30	chr14:39900200-39903000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr14:39900200-39903200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr14:39900200-39903200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr14:39900200-39903200	Active TSS	Pancreas	Pancrea
34	chr14:39900400-39903000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:39900400-39903000	Active TSS	Fetal Kidney	kidney
36	chr14:39900400-39903000	Bivalent/Poised TSS	HepG2	liver
37	chr14:39900400-39903000	Active TSS	K562	blood
38	chr14:39900400-39903200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:39900400-39903200	Active TSS	Fetal Lung	lung
40	chr14:39900400-39903200	Active TSS	NH-A	brain
41	chr14:39900600-39903000	Active TSS	Brain Anterior Caudate	brain
42	chr14:39900600-39903000	Active TSS	Fetal Intestine Small	intestine
43	chr14:39900800-39903200	Active TSS	Fetal Muscle Leg	muscle
44	chr14:39900800-39903200	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr14:39901000-39903000	Active TSS	Fetal Muscle Trunk	muscle
46	chr14:39901200-39903200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:39902000-39903000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr14:39902000-39903000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr14:39902000-39903000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:39902000-39903200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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