Variant report

Variant	rs41272785
Chromosome Location	chr12:48396009-48396010
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	SMARCB1	chr12:48394643-48396159	Hela-S3	cervix:	n/a	n/a
2	MAX	chr12:48394684-48396207	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948 chr12:48395771-48395781
3	FOXA1	chr12:48395710-48396125	T-47D	breast:	n/a	n/a
4	TBP	chr12:48395992-48396031	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXA2	chr12:48395684-48396160	A549	lung:	n/a	n/a
6	GATA3	chr12:48395754-48396385	T-47D	breast:	n/a	n/a
7	MAX	chr12:48395778-48397117	MCF-7	breast:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
8	HA-E2F1	chr12:48395990-48397009	MCF-7	breast:	n/a	n/a
9	FOXA1	chr12:48395730-48396198	HepG2	liver:	n/a	n/a
10	NRF1	chr12:48396003-48397082	SK-N-SH	brain:	n/a	n/a
11	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
12	SIN3A	chr12:48394675-48396247	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOXA2	chr12:48395732-48396143	A549	lung:	n/a	n/a
14	ZBTB7A	chr12:48395036-48396013	ECC-1	luminal epithelium:	n/a	n/a
15	FOXA1	chr12:48395813-48396162	HepG2	liver:	n/a	n/a
16	FOXA1	chr12:48395782-48396134	T-47D	breast:	n/a	n/a
17	TCF12	chr12:48395072-48396101	ECC-1	luminal epithelium:	n/a	chr12:48395173-48395181
18	FOXA2	chr12:48395789-48396125	HepG2	liver:	n/a	n/a
19	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
20	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
21	EP300	chr12:48395773-48396254	T-47D	breast:	n/a	chr12:48395971-48395981
22	TCF7L2	chr12:48395911-48396134	MCF-7	breast:	n/a	n/a
23	YY1	chr12:48395448-48396269	H1-hESC	embryonic stem cell:	n/a	chr12:48395774-48395785 chr12:48396070-48396079 chr12:48395773-48395782 chr12:48396098-48396114
24	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
25	TCF7L2	chr12:48395864-48396189	PANC-1	pancreas:	n/a	n/a
26	ZNF263	chr12:48394775-48396398	HEK293-T-REx	kidney:	n/a	chr12:48396283-48396292
27	GATA3	chr12:48395750-48396205	T-47D	breast:	n/a	n/a
28	MAX	chr12:48394712-48397112	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48396876-48396883 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48396875-48396884 chr12:48394939-48394948 chr12:48395771-48395781 chr12:48396872-48396887
29	CTBP2	chr12:48394745-48396786	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48297374..48299237-chr12:48393563..48396184,2	MCF-7	breast:
2	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
3	chr12:48394829..48397203-chr12:48403090..48404738,2	MCF-7	breast:
4	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
5	chr12:48295052..48296721-chr12:48395942..48397721,2	MCF-7	breast:
6	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
7	chr12:48393914..48396723-chr12:48402943..48405805,2	K562	blood:
8	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:
9	chr12:48356300..48358721-chr12:48393251..48396453,4	MCF-7	breast:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000257985	Chromatin interaction
ENSG00000258203	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11168351	0.84[ASN][1000 genomes]
rs12579815	1.00[EUR][1000 genomes]
rs12580309	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581263	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12819124	0.83[ASN][1000 genomes]
rs17122615	1.00[EUR][1000 genomes]
rs17122617	1.00[EUR][1000 genomes]
rs1814231	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41369448	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60275794	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs915920	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394600-48396200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr12:48394800-48396200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48394800-48396400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
5	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
6	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
8	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
9	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
10	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
11	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:48394800-48397800	Enhancers	Spleen	Spleen
13	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
14	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
15	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:48395000-48396200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
19	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
20	chr12:48395000-48396400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:48395000-48396400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
22	chr12:48395000-48396400	Active TSS	HSMMtube	muscle
23	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
26	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
27	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
28	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Osteobl	bone
29	chr12:48395000-48396800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:48395000-48396800	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
33	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
35	chr12:48395000-48397000	Active TSS	Aorta	Aorta
36	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
41	chr12:48395200-48396200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:48395200-48396400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr12:48395200-48396400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:48395200-48396600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
46	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
48	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain

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