Variant report

Variant	rs55748925
Chromosome Location	chr12:106492583-106492584
allele	A/G
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	HNF4A	chr12:106492377-106492779	HepG2	liver:	n/a	chr12:106492594-106492608 chr12:106492593-106492608
2	MYBL2	chr12:106492381-106493086	HepG2	liver:	n/a	n/a
3	FOXA1	chr12:106492302-106493120	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
4	HNF4G	chr12:106492414-106492760	HepG2	liver:	n/a	chr12:106492594-106492608
5	HNF4G	chr12:106492415-106493067	HepG2	liver:	n/a	chr12:106492594-106492608
6	HNF4A	chr12:106492377-106492993	HepG2	liver:	n/a	chr12:106492594-106492608 chr12:106492593-106492608
7	SPI1	chr12:106492133-106492944	GM12878	blood:	n/a	chr12:106492555-106492568 chr12:106492554-106492567 chr12:106492681-106492694 chr12:106492557-106492566
8	HDAC2	chr12:106492368-106493123	HepG2	liver:	n/a	chr12:106492790-106492804 chr12:106492789-106492803 chr12:106492858-106492867
9	SPI1	chr12:106492383-106492692	GM12878	blood:	n/a	chr12:106492555-106492568 chr12:106492554-106492567 chr12:106492557-106492566
10	EP300	chr12:106492193-106493174	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
11	MYBL2	chr12:106492262-106493183	HepG2	liver:	n/a	n/a
12	HDAC2	chr12:106492347-106493068	HepG2	liver:	n/a	chr12:106492790-106492804 chr12:106492789-106492803 chr12:106492858-106492867
13	SPI1	chr12:106492472-106492617	GM12878	blood:	n/a	chr12:106492555-106492568 chr12:106492554-106492567 chr12:106492557-106492566
14	NR2F2	chr12:106492270-106493243	HepG2	liver:	n/a	n/a
15	TCF7L2	chr12:106492086-106493005	HepG2	liver:	n/a	chr12:106492580-106492596 chr12:106492584-106492594 chr12:106492580-106492596 chr12:106492553-106492560 chr12:106492581-106492595 chr12:106492583-106492592 chr12:106492309-106492323 chr12:106492584-106492593
16	TCF12	chr12:106492371-106493248	A549	lung:	n/a	chr12:106492891-106492900
17	RCOR1	chr12:106492247-106492960	HepG2	liver:	n/a	n/a
18	EP300	chr12:106492317-106493133	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
19	TEAD4	chr12:106492372-106493162	HepG2	liver:	n/a	n/a
20	JUND	chr12:106492459-106492679	HepG2	liver:	n/a	n/a
21	FOXA1	chr12:106492359-106493061	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
22	TCF7L2	chr12:106492212-106492799	PANC-1	pancreas:	n/a	chr12:106492580-106492596 chr12:106492584-106492594 chr12:106492580-106492596 chr12:106492553-106492560 chr12:106492581-106492595 chr12:106492583-106492592 chr12:106492309-106492323 chr12:106492584-106492593
23	HNF4A	chr12:106492354-106493092	HepG2	liver:	n/a	chr12:106492594-106492608 chr12:106492593-106492608
24	MAZ	chr12:106492477-106492931	HepG2	liver:	n/a	n/a
25	ELF1	chr12:106492460-106492770	HepG2	liver:	n/a	n/a
26	FOXA2	chr12:106492290-106493328	HepG2	liver:	n/a	chr12:106492855-106492867
27	JUN	chr12:106492528-106493017	HepG2	liver:	n/a	n/a
28	ELF1	chr12:106492353-106492780	HepG2	liver:	n/a	n/a
29	SPI1	chr12:106492393-106492702	GM12891	blood:	n/a	chr12:106492555-106492568 chr12:106492554-106492567 chr12:106492681-106492694 chr12:106492557-106492566
30	RXRA	chr12:106492411-106493053	HepG2	liver:	n/a	n/a
31	SMC3	chr12:106492334-106492717	HepG2	liver:	n/a	n/a
32	EP300	chr12:106492287-106493003	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
33	CUX1	chr12:106492526-106492604	GM12878	blood:	n/a	n/a
34	NFIC	chr12:106492282-106493149	HepG2	liver:	n/a	chr12:106492342-106492370
35	NR2F2	chr12:106492243-106493215	HepG2	liver:	n/a	n/a
36	SP1	chr12:106492291-106493107	HepG2	liver:	n/a	chr12:106492446-106492460
37	FOXA1	chr12:106492307-106493169	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
38	NFIC	chr12:106492428-106493048	HepG2	liver:	n/a	n/a
39	FOXA1	chr12:106492271-106493197	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
40	ARID3A	chr12:106492366-106493193	HepG2	liver:	n/a	n/a
41	FOXA2	chr12:106492364-106493081	HepG2	liver:	n/a	chr12:106492855-106492867
42	EP300	chr12:106492386-106492644	GM12878	blood:	n/a	n/a
43	RAD21	chr12:106492537-106492955	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:106486379..106488971-chr12:106490561..106492780,2	MCF-7	breast:
2	chr12:106491668..106493233-chr12:106494081..106496361,2	MCF-7	breast:
3	chr12:106325602..106327976-chr12:106491240..106494183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257438	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10492351	0.87[ASN][1000 genomes]
rs11112866	0.87[ASN][1000 genomes]
rs12318540	0.87[ASN][1000 genomes]
rs1896364	0.94[ASN][1000 genomes]
rs3782692	0.93[ASN][1000 genomes]
rs56010291	1.00[AFR][1000 genomes]
rs56027035	0.80[ASN][1000 genomes]
rs7138598	0.87[ASN][1000 genomes]
rs7485023	0.94[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	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
3	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
4	chr12:106481000-106493000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr12:106485200-106500400	Weak transcription	HMEC	breast
6	chr12:106485400-106500800	Weak transcription	Lung	lung
7	chr12:106485600-106496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:106485800-106495000	Strong transcription	HSMMtube	muscle
10	chr12:106486200-106493400	Enhancers	Brain Substantia Nigra	brain
11	chr12:106487200-106492600	Enhancers	Psoas Muscle	Psoas
12	chr12:106487400-106499400	Weak transcription	Brain Germinal Matrix	brain
13	chr12:106487600-106500200	Weak transcription	NHLF	lung
14	chr12:106488600-106495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:106488800-106492800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:106489600-106494600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:106490000-106496800	Weak transcription	Aorta	Aorta
18	chr12:106490200-106492800	Enhancers	Brain Angular Gyrus	brain
19	chr12:106490200-106493400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr12:106490200-106493400	Enhancers	Brain Hippocampus Middle	brain
21	chr12:106490400-106493400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:106490400-106494200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:106490600-106493200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:106490600-106493400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr12:106490600-106494600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:106490600-106498200	Weak transcription	Pancreas	Pancrea
27	chr12:106490800-106493400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr12:106490800-106493400	Enhancers	Brain Cingulate Gyrus	brain
29	chr12:106490800-106494800	Weak transcription	Fetal Stomach	stomach
30	chr12:106490800-106499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:106491000-106493400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:106491000-106493400	Enhancers	Fetal Heart	heart
33	chr12:106491000-106493600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:106491000-106495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:106491000-106496600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:106491000-106499600	Weak transcription	Fetal Kidney	kidney
37	chr12:106491200-106493600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:106491200-106494400	Weak transcription	Adipose Nuclei	Adipose
39	chr12:106491200-106494600	Weak transcription	Gastric	stomach
40	chr12:106491200-106499800	Strong transcription	HSMM	muscle
41	chr12:106491200-106500000	Weak transcription	Fetal Lung	lung
42	chr12:106491200-106500800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:106491400-106492600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:106491400-106492600	Genic enhancers	A549	lung
45	chr12:106491400-106493400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr12:106491400-106495400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:106491400-106496600	Weak transcription	NHDF-Ad	bronchial
48	chr12:106491400-106499600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:106491600-106492800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr12:106491600-106492800	Genic enhancers	Left Ventricle	heart

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