Variant report

Variant	rs9651998
Chromosome Location	chr12:50653962-50653963
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	FOXA1	chr12:50653228-50653978	HepG2	liver:	n/a	n/a
2	TEAD4	chr12:50653194-50653988	HepG2	liver:	n/a	n/a
3	CEBPB	chr12:50653636-50654172	K562	blood:	n/a	chr12:50653986-50653997
4	ELF1	chr12:50653882-50654048	HepG2	liver:	n/a	n/a
5	CEBPB	chr12:50653817-50654111	H1-hESC	embryonic stem cell:	n/a	chr12:50653986-50653997
6	EP300	chr12:50653298-50654053	HepG2	liver:	n/a	n/a
7	ARID3A	chr12:50653261-50654044	HepG2	liver:	n/a	n/a
8	NFIC	chr12:50653160-50654029	ECC-1	luminal epithelium:	n/a	n/a
9	CEBPB	chr12:50653816-50654102	IMR90	lung:	n/a	chr12:50653986-50653997
10	FOXA1	chr12:50653303-50654000	HepG2	liver:	n/a	n/a
11	CEBPB	chr12:50653913-50654054	K562	blood:	n/a	chr12:50653986-50653997
12	CEBPB	chr12:50653864-50654036	HepG2	liver:	n/a	chr12:50653986-50653997
13	NR2F2	chr12:50653349-50654019	HepG2	liver:	n/a	n/a
14	CEBPB	chr12:50653444-50654106	HepG2	liver:	n/a	chr12:50653986-50653997
15	CEBPB	chr12:50653849-50654098	Hela-S3	cervix:	n/a	chr12:50653986-50653997
16	CEBPB	chr12:50653849-50654106	A549	lung:	n/a	chr12:50653986-50653997
17	SP1	chr12:50653356-50654045	HepG2	liver:	n/a	n/a
18	CEBPB	chr12:50653854-50654074	HepG2	liver:	n/a	chr12:50653986-50653997
19	ZNF384	chr12:50653866-50654053	K562	blood:	n/a	n/a
20	FOXA1	chr12:50653261-50654017	HepG2	liver:	n/a	n/a
21	MYBL2	chr12:50653263-50654078	HepG2	liver:	n/a	n/a
22	CEBPB	chr12:50653758-50654157	K562	blood:	n/a	chr12:50653986-50653997
23	CEBPB	chr12:50653683-50654020	ECC-1	luminal epithelium:	n/a	chr12:50653986-50653997

No.	Distal block	Cell Line	Cell type
1	chr12:50637092..50639387-chr12:50653730..50656113,2	K562	blood:
2	chr12:50652124..50654779-chr12:50674069..50676173,2	K562	blood:
3	chr12:50653280..50655917-chr12:50658435..50660402,2	K562	blood:
4	chr12:50572151..50574598-chr12:50653111..50654640,2	K562	blood:
5	chr12:50653700..50656235-chr12:50667803..50669605,2	K562	blood:
6	chr12:50646771..50649988-chr12:50653700..50656765,4	K562	blood:

Variant related genes	Relation type
RNU6-1093P	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10083076	1.00[AMR][1000 genomes]
rs11169403	1.00[AMR][1000 genomes]
rs12297832	1.00[AMR][1000 genomes]
rs12298057	1.00[AMR][1000 genomes]
rs12302910	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12308132	1.00[AMR][1000 genomes]
rs12308735	1.00[AMR][1000 genomes]
rs12312142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314391	1.00[AMR][1000 genomes]
rs12316153	1.00[AMR][1000 genomes]
rs12317780	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318245	1.00[AMR][1000 genomes]
rs7298085	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7305783	1.00[AFR][1000 genomes];1.00[AMR][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
3	chr12:50648800-50668000	Weak transcription	Lung	lung
4	chr12:50649200-50665400	Weak transcription	Aorta	Aorta
5	chr12:50649200-50671000	Weak transcription	Small Intestine	intestine
6	chr12:50649600-50659600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:50650000-50654200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50650400-50654600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr12:50650600-50654000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:50650800-50654600	Enhancers	Stomach Mucosa	stomach
11	chr12:50650800-50655800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:50651000-50654000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr12:50651000-50654200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr12:50651000-50654600	Enhancers	HMEC	breast
15	chr12:50651000-50655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:50651000-50655600	Enhancers	Duodenum Mucosa	Duodenum
17	chr12:50651200-50654000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:50651200-50654000	Enhancers	Osteobl	bone
19	chr12:50651400-50654000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:50651400-50654000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:50651600-50654600	Enhancers	Fetal Intestine Large	intestine
22	chr12:50652200-50654000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:50652200-50654400	Enhancers	Adipose Nuclei	Adipose
24	chr12:50652200-50659600	Weak transcription	Gastric	stomach
25	chr12:50652200-50661800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:50652200-50665400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:50652200-50675800	Weak transcription	Fetal Stomach	stomach
28	chr12:50652400-50654600	Enhancers	Fetal Intestine Small	intestine
29	chr12:50652400-50654600	Enhancers	Hela-S3	cervix
30	chr12:50652400-50656400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:50652400-50656600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:50652400-50657800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:50652400-50664800	Weak transcription	Liver	Liver
34	chr12:50652400-50665200	Weak transcription	NHLF	lung
35	chr12:50652400-50665400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:50652400-50668000	Weak transcription	Left Ventricle	heart
37	chr12:50652400-50671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:50652400-50676200	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:50652400-50676400	Weak transcription	HSMM	muscle
40	chr12:50652800-50654000	Enhancers	Colon Smooth Muscle	Colon
41	chr12:50652800-50654000	Enhancers	Fetal Lung	lung
42	chr12:50653000-50654000	Flanking Active TSS	HepG2	liver
43	chr12:50653000-50665400	Weak transcription	HSMMtube	muscle
44	chr12:50653200-50659600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:50653400-50654000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:50653400-50654000	Enhancers	Ovary	ovary
47	chr12:50653400-50654200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:50653400-50654800	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr12:50653400-50665400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:50653600-50654000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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