Variant report

Variant	rs73297117
Chromosome Location	chr12:48358300-48358301
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	GATA3	chr12:48357852-48358392	T-47D	breast:	n/a	n/a
2	WRNIP1	chr12:48357874-48358497	GM12878	blood:	n/a	n/a
3	RAD21	chr12:48356736-48358455	SK-N-SH	brain:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
4	NFIC	chr12:48357056-48358594	ECC-1	luminal epithelium:	n/a	chr12:48357541-48357557 chr12:48357540-48357557
5	SMARCC1	chr12:48357027-48358349	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr12:48357856-48358310	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr12:48357898-48358306	K562	blood:	n/a	n/a
8	GATA3	chr12:48357878-48358461	T-47D	breast:	n/a	n/a
9	POLR2A	chr12:48357005-48358541	SK-N-MC	brain:	n/a	n/a
10	MAX	chr12:48357006-48358390	MCF-7	breast:	n/a	n/a
11	SMC3	chr12:48356860-48358490	SK-N-SH	brain:	n/a	chr12:48357572-48357582
12	CTCF	chr12:48356634-48358309	A549	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
13	TEAD4	chr12:48357884-48358362	K562	blood:	n/a	n/a
14	BHLHE40	chr12:48357877-48358362	K562	blood:	n/a	n/a
15	SIN3A	chr12:48356997-48358337	H1-hESC	embryonic stem cell:	n/a	chr12:48357581-48357592 chr12:48357246-48357257 chr12:48358317-48358330 chr12:48357052-48357060
16	GATA3	chr12:48357637-48358457	MCF-7	breast:	n/a	n/a
17	CHD1	chr12:48358206-48358371	GM12878	blood:	n/a	n/a
18	SRF	chr12:48357781-48358397	MCF-7	breast:	n/a	chr12:48358129-48358147
19	SRF	chr12:48357880-48358469	MCF-7	breast:	n/a	chr12:48358129-48358147
20	MAX	chr12:48356942-48358344	ECC-1	luminal epithelium:	n/a	n/a
21	ZBTB7A	chr12:48356986-48358355	ECC-1	luminal epithelium:	n/a	chr12:48357554-48357561 chr12:48357685-48357692
22	BHLHE40	chr12:48357983-48358330	HepG2	liver:	n/a	n/a
23	TCF12	chr12:48356984-48358308	ECC-1	luminal epithelium:	n/a	n/a
24	BHLHE40	chr12:48357086-48358385	GM12878	blood:	n/a	n/a
25	USF2	chr12:48358005-48358382	Hela-S3	cervix:	n/a	chr12:48358171-48358182
26	MAX	chr12:48356908-48358365	A549	lung:	n/a	n/a
27	RCOR1	chr12:48356453-48358490	IMR90	lung:	n/a	n/a
28	GATA2	chr12:48357956-48358315	SH-SY5Y	brain:	n/a	n/a
29	TEAD4	chr12:48357905-48358357	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr12:48357003-48358383	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48355845..48358792-chr12:48550018..48552863,2	K562	blood:
2	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
3	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
4	chr12:48099497..48101180-chr12:48357340..48359052,2	K562	blood:

Variant related genes	Relation type
TMEM106C	TF binding region
ENSG00000257433	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000177981	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17122498	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34111422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57138989	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61134963	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73297131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	chr12:48356800-48358400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:48357000-48358400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:48357000-48358400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:48357000-48358400	Active TSS	Esophagus	oesophagus
5	chr12:48357200-48358400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:48357200-48358400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:48357200-48358600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:48357400-48358400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr12:48357600-48358400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48357600-48358400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:48357600-48358400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:48357600-48358400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:48357600-48358400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:48357600-48358400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:48357800-48358400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:48357800-48358400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr12:48357800-48358400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48357800-48358400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr12:48357800-48358400	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr12:48357800-48358400	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr12:48357800-48358400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:48357800-48358400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr12:48357800-48358400	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr12:48357800-48358400	Flanking Active TSS	Placenta	Placenta
25	chr12:48357800-48358400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr12:48357800-48358400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr12:48357800-48358400	Flanking Active TSS	HUVEC	blood vessel
28	chr12:48357800-48358400	Flanking Active TSS	K562	blood
29	chr12:48357800-48358600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:48357800-48358600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr12:48357800-48358600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:48357800-48358600	Flanking Active TSS	Fetal Brain Female	brain
33	chr12:48357800-48358800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:48357800-48358800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr12:48358000-48358400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
36	chr12:48358000-48358400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr12:48358000-48358400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
38	chr12:48358000-48358400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:48358000-48358400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:48358000-48358400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
41	chr12:48358000-48358400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:48358000-48358400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr12:48358000-48358400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr12:48358000-48358400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:48358000-48358400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:48358000-48358400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr12:48358000-48358400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:48358000-48358400	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr12:48358000-48358400	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr12:48358000-48358400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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