Variant report

Variant	rs2239190
Chromosome Location	chr12:48146182-48146183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCC1	chr12:48146110-48149011	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48145973..48147793-chr12:48165632..48167203,2	MCF-7	breast:
4	chr12:48108739..48111513-chr12:48143992..48146721,2	MCF-7	breast:
5	chr12:48145090..48147406-chr12:48155481..48157824,2	K562	blood:
6	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:
7	chr12:48144391..48147829-chr12:48212557..48216683,4	MCF-7	breast:

No data

Variant related genes	Relation type
SLC48A1	TF binding region
RAPGEF3	TF binding region
ENSG00000257433	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs4760653	0.85[EUR][1000 genomes]
rs56199059	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7397585	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7399189	0.87[EUR][1000 genomes]
rs757342	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	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
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
5	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
6	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:48136000-48146200	Weak transcription	Osteobl	bone
9	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:48138000-48148000	Weak transcription	Liver	Liver
11	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:48139400-48147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:48139800-48146600	Weak transcription	Fetal Lung	lung
14	chr12:48139800-48146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:48140200-48146200	Strong transcription	Fetal Stomach	stomach
16	chr12:48140200-48146800	Weak transcription	Fetal Heart	heart
17	chr12:48141200-48147600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:48141600-48147000	Weak transcription	GM12878-XiMat	blood
19	chr12:48141800-48147000	Weak transcription	Primary B cells from cord blood	blood
20	chr12:48143200-48147000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:48143800-48146200	Strong transcription	Fetal Intestine Small	intestine
22	chr12:48143800-48146200	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:48143800-48146600	Weak transcription	Aorta	Aorta
24	chr12:48144200-48146800	Enhancers	HMEC	breast
25	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
28	chr12:48144400-48146200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:48144800-48146200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:48144800-48146400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:48144800-48146800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:48144800-48147400	Weak transcription	Fetal Kidney	kidney
33	chr12:48145000-48149000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:48145200-48146600	Enhancers	Hela-S3	cervix
35	chr12:48145200-48146800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:48145200-48147000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:48145200-48148600	Genic enhancers	Brain Hippocampus Middle	brain
38	chr12:48145200-48148600	Enhancers	Esophagus	oesophagus
39	chr12:48145200-48149000	Enhancers	HSMM	muscle
40	chr12:48145400-48146200	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr12:48145400-48146400	Genic enhancers	Brain Angular Gyrus	brain
42	chr12:48145400-48147200	Weak transcription	Pancreas	Pancrea
43	chr12:48145400-48148400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:48145400-48148400	Genic enhancers	Brain Cingulate Gyrus	brain
45	chr12:48145400-48148800	Enhancers	Left Ventricle	heart
46	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
47	chr12:48145400-48151400	Enhancers	Placenta	Placenta
48	chr12:48145600-48146200	Genic enhancers	Brain Substantia Nigra	brain
49	chr12:48145600-48146200	Weak transcription	HUVEC	blood vessel
50	chr12:48145600-48146400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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