Variant report

Variant	rs73503038
Chromosome Location	chr9:100955882-100955883
allele	A/C
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	CBX3	chr9:100955016-100955978	K562	blood:	n/a	n/a
2	REST	chr9:100954779-100956064	H1-neurons	neurons:	n/a	chr9:100955067-100955080 chr9:100955422-100955435
3	MXI1	chr9:100953878-100956313	IMR90	lung:	n/a	n/a
4	ZNF143	chr9:100955240-100955962	K562	blood:	n/a	chr9:100955493-100955503
5	GTF2F1	chr9:100955221-100955905	Hela-S3	cervix:	n/a	n/a
6	MAX	chr9:100954794-100956011	A549	lung:	n/a	chr9:100955100-100955110
7	FOS	chr9:100955521-100955909	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr9:100954743-100955888	MCF10A-Er-Src	breast:	n/a	n/a
9	BHLHE40	chr9:100954926-100955886	K562	blood:	n/a	n/a
10	POLR2A	chr9:100955842-100958371	K562	blood:	n/a	n/a
11	TFAP2C	chr9:100954915-100955930	Hela-S3	cervix:	n/a	chr9:100955524-100955539
12	MXI1	chr9:100954072-100956277	SK-N-SH	brain:	n/a	n/a
13	WRNIP1	chr9:100955594-100955883	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:100954685-100955927	K562	blood:	n/a	n/a
15	CTCF	chr9:100954592-100956071	SK-N-SH	brain:	n/a	chr9:100955156-100955165 chr9:100955487-100955500 chr9:100955485-100955501 chr9:100955486-100955507 chr9:100954853-100954866 chr9:100955484-100955502
16	POLR2A	chr9:100954941-100955891	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:100883473..100884060-chr9:100955051..100955908,2	MCF-7	breast:
2	chr9:100954775..100957184-chr9:101014893..101018488,3	K562	blood:
3	chr9:100817834..100821135-chr9:100954026..100958556,6	MCF-7	breast:
4	chr9:100933577..100935693-chr9:100955515..100957092,2	MCF-7	breast:
5	chr9:100952914..100958060-chr9:101016344..101019894,9	MCF-7	breast:
6	chr9:100955094..100957753-chr9:101010315..101013161,2	MCF-7	breast:
7	chr9:100951866..100957184-chr9:101014234..101020511,10	K562	blood:
8	chr9:100932527..100936703-chr9:100952110..100957364,6	MCF-7	breast:
9	chr9:100955088..100957656-chr9:100968748..100970804,2	K562	blood:
10	chr9:100919441..100922231-chr9:100955358..100957777,2	MCF-7	breast:
11	chr9:100880288..100886270-chr9:100953608..100957100,8	MCF-7	breast:
12	chr9:100835251..100838541-chr9:100953348..100956508,6	MCF-7	breast:
13	chr9:100877974..100882322-chr9:100953652..100957621,5	K562	blood:

Variant related genes	Relation type
CORO2A	TF binding region
ENSG00000106785	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000106789	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12001270	0.92[EUR][1000 genomes]
rs12344498	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344678	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12349129	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12349172	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16913609	0.94[EUR][1000 genomes]
rs28635946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55710345	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56350443	0.92[EUR][1000 genomes]
rs56675709	0.92[EUR][1000 genomes]
rs57756870	0.92[EUR][1000 genomes]
rs57761120	0.94[EUR][1000 genomes]
rs58302299	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58653026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58762276	0.94[EUR][1000 genomes]
rs60887768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7033797	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73498781	0.92[EUR][1000 genomes]
rs73498784	0.92[EUR][1000 genomes]
rs73657117	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv3415002	chr9:100953931-100956079	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100953800-100956000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr9:100954000-100956000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:100954000-100956000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr9:100954000-100956000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr9:100954200-100956000	Active TSS	Primary T cells from cord blood	blood
6	chr9:100954400-100956000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:100954400-100956000	Active TSS	Brain Cingulate Gyrus	brain
8	chr9:100954400-100956200	Active TSS	Brain Angular Gyrus	brain
9	chr9:100954600-100956000	Active TSS	NHLF	lung
10	chr9:100955200-100956000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr9:100955200-100956000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:100955200-100956000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:100955200-100956000	Flanking Active TSS	Dnd41	blood
14	chr9:100955200-100956000	Flanking Active TSS	GM12878-XiMat	blood
15	chr9:100955400-100956000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:100955400-100956000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr9:100955400-100956000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr9:100955400-100956000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr9:100955400-100956000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr9:100955400-100956000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr9:100955400-100956000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:100955400-100956000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:100955400-100956000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr9:100955400-100956000	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr9:100955400-100956000	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr9:100955400-100956000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr9:100955600-100956000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr9:100955600-100956000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr9:100955600-100956000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr9:100955600-100956000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr9:100955600-100956000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr9:100955600-100956000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr9:100955600-100956000	Flanking Active TSS	A549	lung
34	chr9:100955600-100956000	Flanking Active TSS	HepG2	liver
35	chr9:100955600-100956000	Flanking Active TSS	K562	blood
36	chr9:100955600-100956000	Flanking Active TSS	NHEK	skin
37	chr9:100955600-100956200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:100955600-100956200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:100955600-100956200	Enhancers	Fetal Brain Male	brain
40	chr9:100955600-100956200	Enhancers	Spleen	Spleen
41	chr9:100955600-100956200	Flanking Active TSS	Hela-S3	cervix
42	chr9:100955600-100956800	Enhancers	Lung	lung
43	chr9:100955800-100956000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr9:100955800-100956000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr9:100955800-100956000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr9:100955800-100956000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:100955800-100956000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:100955800-100956000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr9:100955800-100956000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:100955800-100956000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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