Variant report

Variant	rs2238135
Chromosome Location	chr12:48278190-48278191
allele	C/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	NFIC	chr12:48277888-48279460	GM12878	blood:	n/a	n/a
2	IRF4	chr12:48278146-48279337	GM12878	blood:	n/a	n/a
3	NFIC	chr12:48278162-48279394	GM12878	blood:	n/a	n/a
4	EBF1	chr12:48278141-48278569	GM12878	blood:	n/a	n/a
5	MTA3	chr12:48275926-48279701	GM12878	blood:	n/a	n/a
6	BATF	chr12:48278117-48279339	GM12878	blood:	n/a	n/a
7	STAT5A	chr12:48276766-48278210	GM12878	blood:	n/a	chr12:48276886-48276894
8	BCLAF1	chr12:48278146-48279457	GM12878	blood:	n/a	chr12:48278655-48278664 chr12:48278496-48278505

No.	Distal block	Cell Line	Cell type
1	chr12:48276795..48279456-chr12:48285534..48287746,2	MCF-7	breast:
2	chr12:48276825..48278640-chr12:48287655..48289892,3	MCF-7	breast:
3	chr12:48276120..48279378-chr12:48295337..48299363,4	MCF-7	breast:

Variant related genes	Relation type
VDR	TF binding region
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12298585	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48265000-48283200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:48273800-48278800	Enhancers	NHDF-Ad	bronchial
4	chr12:48275000-48279800	Enhancers	Fetal Intestine Large	intestine
5	chr12:48275200-48279200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48275200-48280000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48275200-48280200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:48275600-48278200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:48275600-48278600	Genic enhancers	NHEK	skin
10	chr12:48275600-48279800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:48275800-48278400	Enhancers	Fetal Muscle Trunk	muscle
12	chr12:48275800-48278400	Enhancers	Stomach Mucosa	stomach
13	chr12:48275800-48280000	Enhancers	Fetal Thymus	thymus
14	chr12:48276000-48278200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr12:48276400-48279600	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:48277000-48278800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48277000-48280200	Enhancers	HMEC	breast
18	chr12:48277000-48286200	Weak transcription	Right Atrium	heart
19	chr12:48277200-48278200	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr12:48277200-48278400	Bivalent Enhancer	HepG2	liver
21	chr12:48277200-48279000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:48277200-48279200	Enhancers	Colonic Mucosa	Colon
23	chr12:48277200-48279400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:48277200-48279400	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:48277200-48279600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr12:48277200-48280200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr12:48277200-48289600	Weak transcription	Esophagus	oesophagus
28	chr12:48277200-48290600	Weak transcription	Gastric	stomach
29	chr12:48277200-48295000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:48277400-48278200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:48277400-48278400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:48277400-48278800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr12:48277400-48279000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:48277400-48279000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:48277400-48279400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:48277400-48279400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr12:48277400-48279800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:48277400-48279800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:48277400-48279800	Enhancers	Spleen	Spleen
40	chr12:48277400-48280000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:48277400-48280000	Weak transcription	HSMM	muscle
42	chr12:48277400-48280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:48277400-48280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:48277400-48282200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:48277600-48278200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:48277600-48278400	Enhancers	Small Intestine	intestine
47	chr12:48277600-48278800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:48277600-48278800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:48277600-48278800	Weak transcription	Lung	lung
50	chr12:48277600-48279000	Weak transcription	Osteobl	bone

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