Variant report

Variant	rs73652816
Chromosome Location	chr9:21996780-21996781
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	chr9:21994101-21997363	HEK293	kidney:	n/a	n/a
2	POLR2A	chr9:21992900-21997295	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:21996213-21996835	SK-N-MC	brain:	n/a	n/a
4	ELK4	chr9:21996410-21996862	HEK293	kidney:	n/a	n/a
5	SRF	chr9:21996317-21996837	MCF-7	breast:	n/a	n/a
6	POLR2A	chr9:21993381-21996933	Hela-S3	cervix:	n/a	n/a
7	MAX	chr9:21993127-21996787	Hela-S3	cervix:	n/a	n/a
8	ZNF263	chr9:21994663-21996942	HEK293-T-REx	kidney:	n/a	chr9:21995542-21995563 chr9:21995576-21995597 chr9:21995539-21995548
9	KAP1	chr9:21995561-21997350	HEK293	kidney:	n/a	n/a
10	POLR2A	chr9:21993377-21997195	Hela-S3	cervix:	n/a	n/a
11	FOXP2	chr9:21996435-21996780	SK-N-MC	brain:	n/a	n/a
12	TBP	chr9:21995969-21996803	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr9:21993282-21996959	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr9:21993304-21996841	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr9:21993232-21997071	SK-N-MC	brain:	n/a	n/a
16	SIN3A	chr9:21994720-21997061	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELK4	chr9:21996223-21996836	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:21995575..21999159-chr9:22007136..22010675,4	MCF-7	breast:
2	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
3	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:

Variant related genes	Relation type
CDKN2A	TF binding region
ENSG00000147883	Chromatin interaction
ENSG00000229298	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16935753	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2069420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217980	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217990	1.00[EUR][1000 genomes]
rs3217994	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731205	1.00[EUR][1000 genomes]
rs56235436	0.83[AMR][1000 genomes]
rs60693449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61564778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73650003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652841	0.83[AMR][1000 genomes]
rs73652842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652843	1.00[EUR][1000 genomes]
rs73652845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3492902	chr9:21971026-22006145	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3492901	chr9:21971095-22006263	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21993400-21996800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:21993400-21997000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr9:21993600-21996800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr9:21993800-21996800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr9:21994000-21996800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr9:21995600-21997200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:21995800-21997000	Flanking Active TSS	NH-A	brain
8	chr9:21995800-22008400	Weak transcription	Aorta	Aorta
9	chr9:21996000-21997000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr9:21996000-21997000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr9:21996200-21996800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:21996200-21997200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr9:21996200-21997800	Weak transcription	HSMMtube	muscle
14	chr9:21996200-22004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:21996200-22004000	Weak transcription	Adipose Nuclei	Adipose
16	chr9:21996200-22005200	Weak transcription	Lung	lung
17	chr9:21996200-22005600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:21996400-21996800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
19	chr9:21996400-21997200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr9:21996400-21999000	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr9:21996400-22003000	Weak transcription	HSMM	muscle
22	chr9:21996400-22004200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:21996400-22004400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr9:21996400-22005000	Weak transcription	NHEK	skin
25	chr9:21996400-22005200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:21996400-22005200	Weak transcription	NHDF-Ad	bronchial
27	chr9:21996400-22005200	Weak transcription	Osteobl	bone
28	chr9:21996400-22007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:21996600-21996800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr9:21996600-21996800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:21996600-21996800	Active TSS	GM12878-XiMat	blood
32	chr9:21996600-21996800	Flanking Active TSS	NHLF	lung
33	chr9:21996600-21997000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:21996600-21997200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:21996600-21997200	Flanking Active TSS	Hela-S3	cervix
36	chr9:21996600-21997800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:21996600-21998000	Enhancers	HMEC	breast
38	chr9:21996600-22003000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:21996600-22003800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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