Variant report

Variant	rs539540252
Chromosome Location	chr1:78469359-78469360
allele	A/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	EP300	chr1:78468615-78470834	K562	blood:	n/a	chr1:78469262-78469276
2	ELK1	chr1:78469105-78470507	K562	blood:	n/a	n/a
3	MAFK	chr1:78468708-78470928	K562	blood:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
4	POLR2A	chr1:78469196-78471142	K562	blood:	n/a	n/a
5	ZNF143	chr1:78469193-78470824	K562	blood:	n/a	chr1:78469862-78469880
6	EP300	chr1:78468865-78471212	GM12878	blood:	n/a	chr1:78469262-78469276
7	PML	chr1:78469110-78471238	K562	blood:	n/a	n/a
8	ZNF274	chr1:78469168-78470380	K562	blood:	n/a	n/a
9	MAFK	chr1:78468695-78470840	Hela-S3	cervix:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
10	POLR2A	chr1:78469093-78471037	K562	blood:	n/a	n/a
11	MXI1	chr1:78468827-78470808	K562	blood:	n/a	n/a
12	IRF1	chr1:78468948-78472491	K562	blood:	n/a	chr1:78471360-78471371 chr1:78471672-78471685 chr1:78471360-78471373 chr1:78471361-78471375 chr1:78469905-78469919 chr1:78471360-78471373 chr1:78471359-78471372 chr1:78471674-78471684 chr1:78469257-78469271 chr1:78471360-78471373 chr1:78471360-78471374
13	TBL1XR1	chr1:78468974-78470928	K562	blood:	n/a	n/a
14	POLR2A	chr1:78469161-78472702	MCF10A-Er-Src	breast:	n/a	n/a
15	MAFK	chr1:78468560-78469502	GM12878	blood:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
16	FOS	chr1:78469008-78469454	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:78469047-78471836	PBDE	blood:	n/a	n/a
18	MAFK	chr1:78468865-78469506	IMR90	lung:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
19	MYC	chr1:78469012-78470829	MCF10A-Er-Src	breast:	n/a	n/a
20	BACH1	chr1:78468895-78470495	K562	blood:	n/a	n/a
21	MAFF	chr1:78468968-78469366	HepG2	liver:	n/a	chr1:78469158-78469172 chr1:78469152-78469170
22	JUN	chr1:78468737-78469397	K562	blood:	n/a	n/a
23	POLR2A	chr1:78469014-78471757	Hela-S3	cervix:	n/a	n/a
24	BCLAF1	chr1:78469182-78470943	K562	blood:	n/a	n/a
25	IRF1	chr1:78468673-78471591	K562	blood:	n/a	chr1:78471360-78471371 chr1:78471360-78471373 chr1:78471361-78471375 chr1:78469905-78469919 chr1:78471360-78471373 chr1:78471359-78471372 chr1:78469257-78469271 chr1:78471360-78471373 chr1:78471360-78471374
26	MAFK	chr1:78468959-78469484	HepG2	liver:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
27	ARID3A	chr1:78467855-78472242	K562	blood:	n/a	n/a
28	MAFF	chr1:78468581-78471128	K562	blood:	n/a	chr1:78469158-78469172 chr1:78469152-78469170
29	RFX5	chr1:78469005-78470791	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78222274..78226935-chr1:78467368..78471641,7	K562	blood:
2	chr1:77813619..77816574-chr1:78468319..78470340,2	K562	blood:
3	chr1:45195514..45197967-chr1:78468300..78470449,2	K562	blood:
4	chr1:78469181..78471632-chr1:85154975..85157700,2	K562	blood:
5	chr1:78468129..78475881-chr1:78555411..78565499,18	K562	blood:
6	chr1:78434019..78436134-chr1:78467540..78469438,2	MCF-7	breast:
7	chr1:78468848..78471469-chr13:91999787..92002475,2	K562	blood:
8	chr1:78354412..78357543-chr1:78468778..78471529,4	K562	blood:
9	chr1:78468665..78470165-chr1:80026349..80029039,2	K562	blood:
10	chr1:78147072..78148946-chr1:78468394..78471551,4	K562	blood:
11	chr1:78223538..78227787-chr1:78468626..78471641,9	K562	blood:
12	chr1:78215243..78217892-chr1:78468395..78470149,2	K562	blood:
13	chr1:78466521..78469448-chr1:78786020..78788848,2	K562	blood:
14	chr1:78391278..78394159-chr1:78467798..78470228,4	K562	blood:
15	chr1:78467305..78472459-chr1:78554681..78560615,12	K562	blood:
16	chr1:78469050..78471034-chr12:6647228..6648916,2	K562	blood:
17	chr1:78148235..78150616-chr1:78467949..78471468,6	K562	blood:
18	chr1:78468722..78470321-chr1:110881687..110883282,2	K562	blood:
19	chr1:78466099..78472038-chr1:78511575..78517585,8	K562	blood:
20	chr1:78469253..78470162-chr13:97874132..97874961,2	Hela-S3	cervix:
21	chr1:78469306..78470017-chr6:2841690..2842326,2	Hela-S3	cervix:
22	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
23	chr1:67895339..67897749-chr1:78469184..78471380,2	K562	blood:
24	chr1:78148970..78151388-chr1:78468544..78472172,4	K562	blood:
25	chr1:78391278..78393665-chr1:78467798..78470228,3	K562	blood:
26	chr1:78468395..78470223-chr1:78565706..78567712,2	K562	blood:
27	chr1:78194511..78196220-chr1:78468665..78470167,2	K562	blood:
28	chr1:78196594..78199188-chr1:78468041..78469700,2	K562	blood:
29	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:
30	chr1:78467898..78469708-chr1:78520081..78522686,2	K562	blood:
31	chr1:78245266..78247421-chr1:78469203..78472150,2	K562	blood:
32	chr1:76251016..76253217-chr1:78469296..78471512,3	K562	blood:

Variant related genes	Relation type
DNAJB4	TF binding region
ENSG00000202263	Chromatin interaction
ENSG00000233099	Chromatin interaction
ENSG00000180488	Chromatin interaction
ENSG00000139793	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000269968	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000142864	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000137960	Chromatin interaction
ENSG00000251958	Chromatin interaction
ENSG00000235927	Chromatin interaction
ENSG00000036549	Chromatin interaction
ENSG00000213560	Chromatin interaction
ENSG00000162614	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000222849	Chromatin interaction
ENSG00000021355	Chromatin interaction
ENSG00000162775	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000227963	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv1801396	chr1:78468094-78492221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
2	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78446600-78469600	Weak transcription	Aorta	Aorta
5	chr1:78446600-78469800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:78446600-78470200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:78446600-78470400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:78447600-78469800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:78447600-78470200	Weak transcription	Fetal Brain Male	brain
10	chr1:78447800-78469600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:78450200-78469600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:78450200-78469600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:78452800-78470400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:78452800-78478800	Weak transcription	Spleen	Spleen
16	chr1:78453000-78469600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:78454200-78469800	Weak transcription	Left Ventricle	heart
18	chr1:78454200-78469800	Weak transcription	Psoas Muscle	Psoas
19	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:78454400-78469800	Weak transcription	Right Ventricle	heart
21	chr1:78456200-78470400	Weak transcription	Esophagus	oesophagus
22	chr1:78457400-78469800	Weak transcription	Ovary	ovary
23	chr1:78457400-78470400	Weak transcription	Pancreas	Pancrea
24	chr1:78459400-78469800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:78459600-78469600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:78460000-78469800	Weak transcription	Fetal Thymus	thymus
27	chr1:78460200-78470200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:78461400-78470000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:78461400-78470800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:78461600-78469400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:78461600-78469800	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:78461600-78470000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:78461800-78469800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:78462000-78469400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:78462000-78469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:78462000-78469800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:78462200-78469600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:78462600-78470200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:78463800-78469600	Weak transcription	Fetal Stomach	stomach
40	chr1:78466400-78469600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:78466400-78469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:78467000-78469800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:78468200-78473600	Active TSS	A549	lung
44	chr1:78468400-78469400	Active TSS	Brain Anterior Caudate	brain
45	chr1:78468400-78469600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:78468400-78469600	Flanking Active TSS	Osteobl	bone
47	chr1:78468400-78469800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:78468400-78469800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:78468400-78469800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:78468400-78469800	Enhancers	Hela-S3	cervix

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