Variant report

Variant	rs72823592
Chromosome Location	chr17:46123004-46123005
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	POLR2A	chr17:46122786-46123562	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:46122519-46123550	U87	brain:	n/a	n/a
3	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr17:46122630-46123183	U87	brain:	n/a	n/a
5	POLR2A	chr17:46122734-46126909	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr17:46122711-46123564	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:46122701-46123495	HCT-116	colon:	n/a	n/a
8	STAT3	chr17:46122949-46123582	MCF10A-Er-Src	breast:	n/a	chr17:46123278-46123289 chr17:46123034-46123046 chr17:46123211-46123223 chr17:46123280-46123288 chr17:46123192-46123204
9	POLR2A	chr17:46122744-46123115	MCF-7	breast:	n/a	n/a
10	POLR2A	chr17:46122982-46123329	HCT-116	colon:	n/a	n/a
11	ZNF263	chr17:46122681-46123134	HEK293-T-REx	kidney:	n/a	n/a
12	MYC	chr17:46122917-46123503	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr17:46122485-46124228	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr17:46122554-46123151	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr17:46122512-46124013	PFSK-1	brain:	n/a	n/a
16	FOS	chr17:46122898-46123460	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr17:46121736-46126744	K562	blood:	n/a	n/a
18	STAT3	chr17:46122924-46123484	MCF10A-Er-Src	breast:	n/a	chr17:46123278-46123289 chr17:46123034-46123046 chr17:46123211-46123223 chr17:46123280-46123288 chr17:46123192-46123204
19	JUN	chr17:46122472-46126784	K562	blood:	n/a	chr17:46125601-46125610 chr17:46125499-46125508 chr17:46124562-46124569 chr17:46124562-46124571 chr17:46125676-46125685 chr17:46124353-46124365
20	JUND	chr17:46122940-46123318	K562	blood:	n/a	n/a
21	MYC	chr17:46122942-46123461	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr17:46122440-46123145	SK-N-SH	brain:	n/a	n/a
23	FOS	chr17:46122945-46123399	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr17:46122982-46123525	MCF10A-Er-Src	breast:	n/a	chr17:46123278-46123289 chr17:46123034-46123046 chr17:46123211-46123223 chr17:46123280-46123288 chr17:46123192-46123204
25	POLR2A	chr17:46122545-46123198	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr17:46122525-46123471	U87	brain:	n/a	n/a
27	MAZ	chr17:46123003-46123401	K562	blood:	n/a	n/a
28	FOS	chr17:46122914-46123461	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46120967..46123256-chr17:46183656..46186285,2	MCF-7	breast:
2	chr17:46120800..46123915-chr17:46177973..46180193,3	MCF-7	breast:
3	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPZ2-1	chr17:46122503-46125412	ENSG00000263412.1

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs41280120	0.87[EUR][1000 genomes]
rs7216504	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823527	0.86[EUR][1000 genomes]
rs72823530	0.87[EUR][1000 genomes]
rs72823534	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823591	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823599	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72823601	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72825504	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72825512	0.81[AMR][1000 genomes]
rs8067005	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8073371	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Epilepsy (generalized)	22949513	GWAS catalog

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46115800-46123200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:46115800-46123200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
5	chr17:46119400-46123400	Weak transcription	A549	lung
6	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:46120600-46124200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:46120600-46124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:46121200-46123400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:46121800-46124400	Enhancers	Fetal Muscle Leg	muscle
11	chr17:46122400-46123200	Enhancers	Psoas Muscle	Psoas
12	chr17:46122400-46123400	Enhancers	HSMMtube	muscle
13	chr17:46122400-46124000	Weak transcription	Primary T cells from cord blood	blood
14	chr17:46122400-46124200	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:46122400-46124400	Enhancers	Adipose Nuclei	Adipose
16	chr17:46122600-46123200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:46122600-46123400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:46122600-46123400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:46122600-46123600	Enhancers	K562	blood
20	chr17:46122600-46124000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr17:46122600-46124000	Enhancers	Esophagus	oesophagus
22	chr17:46122600-46124000	Enhancers	HMEC	breast
23	chr17:46122600-46124200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:46122600-46124200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:46122600-46124400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:46122600-46124800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:46122600-46124800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr17:46122600-46124800	Flanking Active TSS	HSMM	muscle
29	chr17:46122600-46125000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:46122800-46123200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr17:46122800-46123200	Enhancers	Placenta	Placenta
32	chr17:46122800-46123200	Enhancers	Osteobl	bone
33	chr17:46122800-46123400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr17:46122800-46123400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr17:46122800-46123400	Enhancers	Lung	lung
36	chr17:46122800-46123400	Enhancers	GM12878-XiMat	blood
37	chr17:46122800-46123600	Weak transcription	NH-A	brain
38	chr17:46122800-46123800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:46122800-46123800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:46122800-46123800	Enhancers	Hela-S3	cervix
41	chr17:46122800-46124000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:46122800-46124000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr17:46122800-46124000	Enhancers	Fetal Heart	heart
44	chr17:46122800-46124200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:46122800-46124200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:46122800-46124200	Enhancers	Fetal Thymus	thymus
47	chr17:46122800-46124200	Enhancers	Stomach Smooth Muscle	stomach
48	chr17:46122800-46124400	Enhancers	Colonic Mucosa	Colon
49	chr17:46122800-46124400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr17:46122800-46124400	Enhancers	Right Atrium	heart

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