Variant report

Variant	rs62041346
Chromosome Location	chr16:79803833-79803834
allele	C/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	RFX5	chr16:79803570-79805472	IMR90	lung:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625
2	POLR2A	chr16:79803819-79804665	PFSK-1	brain:	n/a	n/a
3	MXI1	chr16:79803755-79805133	SK-N-SH	brain:	n/a	n/a
4	ZMIZ1	chr16:79803430-79805584	K562	blood:	n/a	n/a
5	POLR2A	chr16:79803019-79805255	K562	blood:	n/a	n/a
6	EP300	chr16:79802602-79805391	SK-N-SH	brain:	n/a	chr16:79802820-79802834 chr16:79803941-79803955 chr16:79802825-79802839
7	MAZ	chr16:79803269-79804943	K562	blood:	n/a	n/a
8	POLR2A	chr16:79803767-79805282	K562	blood:	n/a	n/a
9	BHLHE40	chr16:79803209-79805113	K562	blood:	n/a	n/a
10	POLR2A	chr16:79803267-79805449	K562	blood:	n/a	n/a
11	RCOR1	chr16:79803113-79805441	K562	blood:	n/a	n/a
12	ZNF384	chr16:79803725-79805000	K562	blood:	n/a	n/a
13	MYC	chr16:79803005-79805009	K562	blood:	n/a	n/a
14	E2F4	chr16:79803811-79804005	MCF10A-Er-Src	breast:	n/a	n/a
15	RFX5	chr16:79803164-79806271	SK-N-SH	brain:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625
16	POLR2A	chr16:79803677-79804863	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000260876	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12443838	1.00[ASN][1000 genomes]
rs4313818	1.00[ASN][1000 genomes]
rs4506911	0.92[ASN][1000 genomes]
rs56006814	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56052219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041304	0.83[AFR][1000 genomes]
rs62041307	1.00[AFR][1000 genomes]
rs62041308	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041309	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041310	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041311	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041312	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041313	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041316	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041317	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041318	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041319	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041320	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62041323	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62041324	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041325	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62041327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041345	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62041347	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62041348	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62041349	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62043341	0.83[AFR][1000 genomes]
rs62043342	0.83[AFR][1000 genomes]
rs62043343	0.83[AFR][1000 genomes]
rs62043344	1.00[AFR][1000 genomes]
rs62043358	0.83[AFR][1000 genomes]
rs7187139	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8053535	0.93[EUR][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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79792800-79804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:79801200-79804200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:79801400-79805000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr16:79801600-79804000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:79801600-79804000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr16:79801600-79804000	Enhancers	Primary hematopoietic stem cells	blood
7	chr16:79801600-79804000	Enhancers	Esophagus	oesophagus
8	chr16:79801600-79804000	Enhancers	Fetal Kidney	kidney
9	chr16:79801600-79804000	Enhancers	Placenta	Placenta
10	chr16:79801600-79804000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr16:79801600-79804400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:79801800-79804000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:79801800-79804000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:79802000-79804000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:79802000-79804000	Enhancers	Primary T cells from cord blood	blood
16	chr16:79802000-79804000	Enhancers	Pancreas	Pancrea
17	chr16:79802000-79804000	Enhancers	Spleen	Spleen
18	chr16:79802200-79804000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr16:79802200-79804000	Enhancers	Stomach Mucosa	stomach
20	chr16:79802400-79804000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr16:79802400-79804000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr16:79802400-79804000	Enhancers	Fetal Muscle Trunk	muscle
23	chr16:79802400-79804000	Enhancers	Fetal Stomach	stomach
24	chr16:79802400-79804000	Enhancers	Left Ventricle	heart
25	chr16:79802400-79804000	Enhancers	Small Intestine	intestine
26	chr16:79802400-79804200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr16:79802600-79804000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr16:79802600-79804000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:79802600-79804000	Enhancers	Brain Cingulate Gyrus	brain
30	chr16:79802600-79804000	Enhancers	Fetal Brain Male	brain
31	chr16:79802600-79804000	Enhancers	Lung	lung
32	chr16:79802600-79804000	Enhancers	NHEK	skin
33	chr16:79802800-79804000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr16:79802800-79804000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:79802800-79804000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:79802800-79804000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:79802800-79804000	Enhancers	Brain Angular Gyrus	brain
38	chr16:79802800-79804000	Enhancers	Brain Anterior Caudate	brain
39	chr16:79802800-79804000	Enhancers	Brain Hippocampus Middle	brain
40	chr16:79802800-79804000	Enhancers	Brain Substantia Nigra	brain
41	chr16:79802800-79804000	Weak transcription	Ovary	ovary
42	chr16:79802800-79804000	Enhancers	Right Ventricle	heart
43	chr16:79802800-79804000	Enhancers	HMEC	breast
44	chr16:79802800-79804000	Weak transcription	HSMM	muscle
45	chr16:79802800-79804000	Enhancers	NHDF-Ad	bronchial
46	chr16:79802800-79804000	Enhancers	NHLF	lung
47	chr16:79803000-79804000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:79803000-79804000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr16:79803000-79804000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr16:79803000-79804000	Enhancers	Brain Inferior Temporal Lobe	brain

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