Variant report

Variant	rs72823591
Chromosome Location	chr17:46122628-46122629
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	POLR2A	chr17:46122519-46123550	U87	brain:	n/a	n/a
2	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr17:46122485-46124228	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:46122554-46123151	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr17:46122512-46124013	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:46121736-46126744	K562	blood:	n/a	n/a
7	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
8	POLR2A	chr17:46122440-46123145	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr17:46122545-46123198	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr17:46122525-46123471	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46120967..46123256-chr17:46183656..46186285,2	MCF-7	breast:
2	chr17:46120800..46123915-chr17:46177973..46180193,3	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: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10514938	1.00[ASN][1000 genomes]
rs11650615	1.00[ASN][1000 genomes]
rs16952265	1.00[ASN][1000 genomes]
rs16953235	1.00[ASN][1000 genomes]
rs16953382	1.00[ASN][1000 genomes]
rs16953461	1.00[ASN][1000 genomes]
rs16953925	1.00[ASN][1000 genomes]
rs16954078	1.00[ASN][1000 genomes]
rs16954204	1.00[ASN][1000 genomes]
rs41280120	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41336845	1.00[ASN][1000 genomes]
rs7216504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823509	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72823513	0.82[EUR][1000 genomes]
rs72823527	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823530	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823534	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823592	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823594	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72823599	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823601	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825504	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825512	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825517	1.00[ASN][1000 genomes]
rs72825548	1.00[ASN][1000 genomes]
rs72825584	1.00[ASN][1000 genomes]
rs8067005	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073371	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46115800-46122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:46115800-46122800	Weak transcription	Brain Anterior Caudate	brain
4	chr17:46115800-46122800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:46115800-46123200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:46115800-46123200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:46116000-46123000	Weak transcription	NHLF	lung
8	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:46119400-46123400	Weak transcription	A549	lung
10	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:46120200-46122800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:46120200-46123000	Enhancers	NHDF-Ad	bronchial
13	chr17:46120600-46122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:46120600-46124200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:46120600-46124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:46120800-46122800	Weak transcription	Placenta	Placenta
17	chr17:46121200-46123400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:46121400-46122800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:46121600-46122800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr17:46121800-46122800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:46121800-46124400	Enhancers	Fetal Muscle Leg	muscle
22	chr17:46122400-46122800	Enhancers	NHEK	skin
23	chr17:46122400-46123200	Enhancers	Psoas Muscle	Psoas
24	chr17:46122400-46123400	Enhancers	HSMMtube	muscle
25	chr17:46122400-46124000	Weak transcription	Primary T cells from cord blood	blood
26	chr17:46122400-46124200	Enhancers	Fetal Muscle Trunk	muscle
27	chr17:46122400-46124400	Enhancers	Adipose Nuclei	Adipose
28	chr17:46122600-46122800	Enhancers	NH-A	brain
29	chr17:46122600-46122800	Flanking Active TSS	Osteobl	bone
30	chr17:46122600-46123000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:46122600-46123000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:46122600-46123000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr17:46122600-46123000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:46122600-46123200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:46122600-46123400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:46122600-46123400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr17:46122600-46123600	Enhancers	K562	blood
38	chr17:46122600-46124000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr17:46122600-46124000	Enhancers	Esophagus	oesophagus
40	chr17:46122600-46124000	Enhancers	HMEC	breast
41	chr17:46122600-46124200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:46122600-46124200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:46122600-46124400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:46122600-46124800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:46122600-46124800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr17:46122600-46124800	Flanking Active TSS	HSMM	muscle
47	chr17:46122600-46125000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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