Variant report

Variant	rs10821275
Chromosome Location	chr9:96721648-96721649
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	SUZ12	chr9:96719499-96722002	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr9:96720002-96722078	H1-hESC	embryonic stem cell:	n/a	n/a
3	EBF1	chr9:96721546-96721785	GM12878	blood:	n/a	chr9:96721664-96721673 chr9:96721664-96721673 chr9:96721664-96721674 chr9:96721663-96721674 chr9:96721662-96721675
4	BACH1	chr9:96721526-96721713	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:96720863-96722645	H1-neurons	neurons:	n/a	n/a
6	MYC	chr9:96720666-96721854	NB4	blood:	n/a	chr9:96720728-96720738
7	HMGN3	chr9:96721641-96721955	K562	blood:	n/a	n/a
8	EBF1	chr9:96721507-96721798	GM12878	blood:	n/a	chr9:96721664-96721673 chr9:96721664-96721673 chr9:96721664-96721674 chr9:96721663-96721674 chr9:96721662-96721675
9	SPI1	chr9:96721458-96721975	HL-60	blood:	n/a	n/a
10	POLR2A	chr9:96720912-96723257	H1-neurons	neurons:	n/a	n/a
11	MAX	chr9:96720726-96721837	NB4	blood:	n/a	chr9:96720728-96720738
12	POLR2A	chr9:96720592-96721841	NB4	blood:	n/a	n/a
13	SUZ12	chr9:96720177-96723275	NT2-D1	testis:	n/a	n/a
14	EBF1	chr9:96721559-96721806	GM12878	blood:	n/a	chr9:96721664-96721673 chr9:96721664-96721673 chr9:96721664-96721674 chr9:96721663-96721674 chr9:96721662-96721675

No.	Distal block	Cell Line	Cell type
1	chr9:96712713..96719267-chr9:96721537..96727951,10	MCF-7	breast:
2	chr9:96442742..96446259-chr9:96719078..96722660,3	MCF-7	breast:
3	chr9:96720222..96721910-chr9:96722308..96724040,2	MCF-7	breast:

Variant related genes	Relation type
BARX1	TF binding region
ENSG00000131668	Chromatin interaction
ENSG00000235601	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1057715	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10821279	0.94[EUR][1000 genomes]
rs10992998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10992999	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993002	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10993004	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993005	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993006	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993007	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993012	0.91[EUR][1000 genomes]
rs10993013	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993015	0.86[EUR][1000 genomes]
rs10993016	0.94[EUR][1000 genomes]
rs12156437	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12375599	0.94[EUR][1000 genomes]
rs1316935	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16909605	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933683	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4269597	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4330748	0.94[EUR][1000 genomes]
rs57693373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59397123	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72755516	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72755517	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73519466	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised 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
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96718400-96722000	Weak transcription	Hela-S3	cervix
2	chr9:96719200-96722000	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr9:96720400-96723200	Bivalent Enhancer	Placenta	Placenta
4	chr9:96720400-96724400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:96720600-96721800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:96720600-96721800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
8	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
10	chr9:96720600-96722000	Bivalent Enhancer	Fetal Brain Male	brain
11	chr9:96720600-96723200	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr9:96720600-96723400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:96720600-96723600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
18	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
19	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr9:96720800-96723200	Bivalent Enhancer	Spleen	Spleen
21	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
23	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chr9:96721000-96721800	Bivalent Enhancer	Psoas Muscle	Psoas
26	chr9:96721000-96722000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
27	chr9:96721000-96722000	Bivalent Enhancer	Fetal Heart	heart
28	chr9:96721000-96722000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr9:96721200-96721800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:96721200-96721800	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr9:96721200-96721800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
32	chr9:96721200-96722000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:96721200-96722000	Active TSS	Aorta	Aorta
34	chr9:96721200-96722000	Flanking Bivalent TSS/Enh	Right Ventricle	heart
35	chr9:96721200-96723000	Enhancers	Pancreas	Pancrea
36	chr9:96721200-96723200	Bivalent Enhancer	Liver	Liver
37	chr9:96721200-96723600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr9:96721200-96723600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr9:96721200-96724200	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr9:96721400-96721800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:96721400-96721800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:96721400-96721800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr9:96721400-96721800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
44	chr9:96721400-96721800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
45	chr9:96721400-96721800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:96721400-96722000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
47	chr9:96721400-96722000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
48	chr9:96721400-96722000	Bivalent Enhancer	Lung	lung
49	chr9:96721400-96722000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
50	chr9:96721400-96722200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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