Variant report

Variant	rs12553205
Chromosome Location	chr9:97401991-97401992
allele	A/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	chr9:97400938-97402355	HL-60	blood:	n/a	n/a
2	HDAC2	chr9:97400903-97402384	MCF-7	breast:	n/a	chr9:97401213-97401221
3	POLR2A	chr9:97401275-97402133	ProgFib	skin:	n/a	n/a
4	ELF1	chr9:97401024-97402322	MCF-7	breast:	n/a	chr9:97401849-97401861
5	POLR2A	chr9:97401009-97402322	MCF-7	breast:	n/a	n/a
6	FOXM1	chr9:97401198-97402230	MCF-7	breast:	n/a	n/a
7	MAX	chr9:97400579-97402724	MCF-7	breast:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
8	E2F6	chr9:97401053-97402004	H1-hESC	embryonic stem cell:	n/a	chr9:97401976-97401986 chr9:97401850-97401859 chr9:97401960-97401969 chr9:97401802-97401812
9	MAX	chr9:97401158-97402292	ECC-1	luminal epithelium:	n/a	chr9:97402273-97402284 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
10	POLR2A	chr9:97401222-97402296	MCF-7	breast:	n/a	n/a
11	MYC	chr9:97401759-97402400	NB4	blood:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
12	NR2F2	chr9:97401299-97402260	MCF-7	breast:	n/a	n/a
13	MAX	chr9:97401229-97402727	H1-hESC	embryonic stem cell:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
14	HA-E2F1	chr9:97401093-97402062	MCF-7	breast:	n/a	chr9:97401976-97401986 chr9:97401850-97401859 chr9:97401960-97401969 chr9:97401802-97401812
15	SIN3A	chr9:97401850-97402686	H1-hESC	embryonic stem cell:	n/a	chr9:97401972-97401983
16	POLR2A	chr9:97401061-97402267	MCF-7	breast:	n/a	n/a
17	MAX	chr9:97401171-97402041	MCF-7	breast:	n/a	chr9:97401961-97401971 chr9:97401965-97401974
18	SIN3AK20	chr9:97400822-97402382	MCF-7	breast:	n/a	n/a
19	TCF12	chr9:97401029-97402221	MCF-7	breast:	n/a	chr9:97401976-97401986
20	HDAC2	chr9:97401247-97402098	MCF-7	breast:	n/a	n/a
21	MAX	chr9:97401350-97402324	ECC-1	luminal epithelium:	n/a	chr9:97402273-97402284 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
22	SUZ12	chr9:97400708-97402723	NT2-D1	testis:	n/a	n/a
23	NR2F2	chr9:97400853-97402433	MCF-7	breast:	n/a	n/a
24	SIN3AK20	chr9:97401000-97402128	MCF-7	breast:	n/a	n/a
25	CEBPB	chr9:97401295-97402332	MCF-7	breast:	n/a	n/a
26	MAX	chr9:97401851-97402541	NB4	blood:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
27	TCF12	chr9:97401171-97402007	ECC-1	luminal epithelium:	n/a	chr9:97401976-97401986

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96927010..96929542-chr9:97400485..97402088,2	MCF-7	breast:
2	chr9:97316754..97318987-chr9:97400777..97403144,3	MCF-7	breast:

Variant related genes	Relation type
FBP1	TF binding region
ENSG00000231806	Chromatin interaction
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs28369693	0.89[EUR][1000 genomes]
rs6479557	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh 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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97400200-97402200	Active TSS	Liver	Liver
2	chr9:97400400-97402000	Active TSS	Stomach Mucosa	stomach
3	chr9:97400600-97402200	Bivalent/Poised TSS	Fetal Kidney	kidney
4	chr9:97400600-97402200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr9:97400600-97402400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:97400800-97402200	Active TSS	Gastric	stomach
7	chr9:97401000-97402000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:97401000-97402200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
9	chr9:97401000-97402400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr9:97401000-97402400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr9:97401000-97402400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:97401000-97402400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr9:97401000-97402400	Active TSS	Right Atrium	heart
14	chr9:97401000-97402600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr9:97401000-97402600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr9:97401000-97402600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:97401000-97402600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:97401000-97402600	Active TSS	Rectal Smooth Muscle	rectum
19	chr9:97401000-97402800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr9:97401000-97402800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr9:97401000-97403000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr9:97401200-97402000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
23	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:97401200-97402200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
25	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:97401200-97402200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:97401200-97402200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr9:97401200-97402200	Active TSS	Small Intestine	intestine
30	chr9:97401200-97402400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr9:97401200-97402400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr9:97401200-97402400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr9:97401200-97402600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:97401200-97402600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr9:97401400-97402000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr9:97401400-97402000	Active TSS	Fetal Intestine Small	intestine
39	chr9:97401400-97402000	Active TSS	Spleen	Spleen
40	chr9:97401400-97402200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:97401400-97402200	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr9:97401400-97402200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:97401400-97402200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr9:97401400-97402200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr9:97401400-97402200	Active TSS	Aorta	Aorta
46	chr9:97401400-97402200	Active TSS	Brain Substantia Nigra	brain
47	chr9:97401400-97402200	Active TSS	Fetal Lung	lung
48	chr9:97401400-97402400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:97401400-97402400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:97401400-97402400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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