Variant report

Variant	rs4417373
Chromosome Location	chr12:48357756-48357757
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	MAX	chr12:48357085-48357823	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr12:48357131-48357937	PANC-1	pancreas:	n/a	n/a
3	HA-E2F1	chr12:48356936-48357780	MCF-7	breast:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452 chr12:48357366-48357377
4	ZEB1	chr12:48357554-48357898	GM12878	blood:	n/a	chr12:48357749-48357758
5	RAD21	chr12:48356736-48358455	SK-N-SH	brain:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
6	NFIC	chr12:48357056-48358594	ECC-1	luminal epithelium:	n/a	chr12:48357541-48357557 chr12:48357540-48357557
7	MYC	chr12:48357683-48357791	MCF-7	breast:	n/a	n/a
8	SMARCC1	chr12:48357027-48358349	Hela-S3	cervix:	n/a	n/a
9	MAX	chr12:48357021-48357810	A549	lung:	n/a	n/a
10	MAX	chr12:48357043-48357865	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr12:48357087-48357781	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:48357005-48358541	SK-N-MC	brain:	n/a	n/a
13	CTCF	chr12:48356824-48357775	SK-N-SH	brain:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
14	E2F6	chr12:48357151-48357800	K562	blood:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357788-48357797 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452
15	E2F6	chr12:48357057-48357828	A549	lung:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357788-48357797 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452
16	MAX	chr12:48357006-48358390	MCF-7	breast:	n/a	n/a
17	E2F6	chr12:48357072-48357915	H1-hESC	embryonic stem cell:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357788-48357797 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452
18	CTBP2	chr12:48357081-48358012	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr12:48356924-48357775	H1-hESC	embryonic stem cell:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
20	TCF12	chr12:48356881-48358078	A549	lung:	n/a	n/a
21	MAX	chr12:48357091-48357785	HepG2	liver:	n/a	n/a
22	ELF1	chr12:48357078-48357837	GM12878	blood:	n/a	n/a
23	SMC3	chr12:48356860-48358490	SK-N-SH	brain:	n/a	chr12:48357572-48357582
24	CTCF	chr12:48356634-48358309	A549	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
25	SMARCB1	chr12:48357054-48358198	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr12:48357011-48357757	K562	blood:	n/a	n/a
27	PML	chr12:48356998-48357769	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:48357100-48358182	ECC-1	luminal epithelium:	n/a	n/a
29	MAZ	chr12:48356891-48357817	IMR90	lung:	n/a	n/a
30	SIN3A	chr12:48356997-48358337	H1-hESC	embryonic stem cell:	n/a	chr12:48357581-48357592 chr12:48357246-48357257 chr12:48358317-48358330 chr12:48357052-48357060
31	TAF1	chr12:48357006-48358049	ECC-1	luminal epithelium:	n/a	n/a
32	GATA3	chr12:48357637-48358457	MCF-7	breast:	n/a	n/a
33	POLR2A	chr12:48357169-48357775	MCF-7	breast:	n/a	n/a
34	HMGN3	chr12:48357085-48357830	K562	blood:	n/a	n/a
35	POLR2A	chr12:48357237-48357863	HepG2	liver:	n/a	n/a
36	MAX	chr12:48357100-48357847	MCF-7	breast:	n/a	n/a
37	MAX	chr12:48356942-48358344	ECC-1	luminal epithelium:	n/a	n/a
38	ZBTB7A	chr12:48356986-48358355	ECC-1	luminal epithelium:	n/a	chr12:48357554-48357561 chr12:48357685-48357692
39	POLR2A	chr12:48357042-48357762	Hela-S3	cervix:	n/a	n/a
40	TCF12	chr12:48356984-48358308	ECC-1	luminal epithelium:	n/a	n/a
41	TEAD4	chr12:48357015-48357761	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr12:48357074-48357809	HepG2	liver:	n/a	n/a
43	MAX	chr12:48357001-48357771	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr12:48357093-48357907	H1-hESC	embryonic stem cell:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357788-48357797 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452
45	BHLHE40	chr12:48357086-48358385	GM12878	blood:	n/a	n/a
46	MAX	chr12:48356908-48358365	A549	lung:	n/a	n/a
47	RCOR1	chr12:48356453-48358490	IMR90	lung:	n/a	n/a
48	MAX	chr12:48357011-48358171	NB4	blood:	n/a	n/a
49	POLR2A	chr12:48357046-48357769	U87	brain:	n/a	n/a
50	REST	chr12:48356909-48357874	H1-neurons	neurons:	n/a	chr12:48357100-48357108

No.	Distal block	Cell Line	Cell type
1	chr12:48298691..48299776-chr12:48356759..48358181,8	MCF-7	breast:
2	chr12:48355845..48358792-chr12:48550018..48552863,2	K562	blood:
3	chr12:48355857..48357881-chr12:48473283..48476045,2	MCF-7	breast:
4	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
5	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
6	chr12:48099497..48101180-chr12:48357340..48359052,2	K562	blood:

Variant related genes	Relation type
TMEM106C	TF binding region
ENSG00000111424	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000222635	Chromatin interaction

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

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

rs_ID	r²[population]
rs12426835	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1635560	0.96[ASN][1000 genomes]
rs2071356	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2898045	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4237856	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4307775	0.82[AMR][1000 genomes]
rs4344559	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4366552	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4494361	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57624904	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs740025	0.89[AMR][1000 genomes];0.87[EUR][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48356800-48357800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:48356800-48357800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:48356800-48357800	Active TSS	Fetal Brain Female	brain
4	chr12:48356800-48358000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr12:48356800-48358000	Active TSS	Colon Smooth Muscle	Colon
6	chr12:48356800-48358000	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:48356800-48358400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:48357000-48357800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:48357000-48357800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
10	chr12:48357000-48357800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:48357000-48358000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:48357000-48358000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:48357000-48358000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:48357000-48358000	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:48357000-48358000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:48357000-48358000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48357000-48358000	Active TSS	Liver	Liver
18	chr12:48357000-48358000	Active TSS	Colonic Mucosa	Colon
19	chr12:48357000-48358000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr12:48357000-48358000	Active TSS	Gastric	stomach
21	chr12:48357000-48358000	Active TSS	Left Ventricle	heart
22	chr12:48357000-48358000	Active TSS	Ovary	ovary
23	chr12:48357000-48358000	Active TSS	Pancreas	Pancrea
24	chr12:48357000-48358000	Active TSS	Psoas Muscle	Psoas
25	chr12:48357000-48358000	Active TSS	Right Atrium	heart
26	chr12:48357000-48358000	Active TSS	NHDF-Ad	bronchial
27	chr12:48357000-48358000	Active TSS	NHLF	lung
28	chr12:48357000-48358200	Active TSS	Aorta	Aorta
29	chr12:48357000-48358200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:48357000-48358400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48357000-48358400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:48357000-48358400	Active TSS	Esophagus	oesophagus
33	chr12:48357200-48357800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:48357200-48357800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:48357200-48357800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:48357200-48357800	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr12:48357200-48357800	Active TSS	Primary B cells from peripheral blood	blood
38	chr12:48357200-48357800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:48357200-48357800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr12:48357200-48357800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:48357200-48357800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:48357200-48357800	Active TSS	Brain Angular Gyrus	brain
43	chr12:48357200-48357800	Active TSS	Brain Anterior Caudate	brain
44	chr12:48357200-48357800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr12:48357200-48357800	Active TSS	Placenta	Placenta
46	chr12:48357200-48357800	Active TSS	Placenta Amnion	Placenta Amnion
47	chr12:48357200-48357800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr12:48357200-48357800	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:48357200-48357800	Active TSS	HSMMtube	muscle
50	chr12:48357200-48357800	Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links