Variant report

Variant	rs56199059
Chromosome Location	chr12:48141798-48141799
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	POLR2A	chr12:48141709-48141800	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:48140978..48143189-chr12:48143371..48145379,2	K562	blood:
2	chr12:48140159..48142599-chr12:48142901..48147506,4	MCF-7	breast:
3	chr12:48135601..48138663-chr12:48139025..48142154,4	K562	blood:
4	chr12:48141723..48143940-chr12:48213579..48216155,2	MCF-7	breast:
5	chr12:48140656..48143910-chr12:48166841..48170698,6	K562	blood:
6	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
7	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

No data

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

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11609044	0.82[EUR][1000 genomes]
rs11615078	0.84[EUR][1000 genomes]
rs12580458	0.83[EUR][1000 genomes]
rs2074535	0.85[EUR][1000 genomes]
rs2238143	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2239190	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5006306	0.83[EUR][1000 genomes]
rs61917615	0.83[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:66 , 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	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
4	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
5	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
8	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
10	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:48135800-48145400	Weak transcription	NHDF-Ad	bronchial
13	chr12:48136000-48146200	Weak transcription	Osteobl	bone
14	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:48136600-48142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:48137400-48142000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:48137800-48145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:48138000-48144200	Weak transcription	Pancreas	Pancrea
19	chr12:48138000-48148000	Weak transcription	Liver	Liver
20	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:48138600-48142000	Weak transcription	HMEC	breast
22	chr12:48138800-48142000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:48139000-48143200	Enhancers	Primary B cells from peripheral blood	blood
24	chr12:48139400-48145200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:48139400-48146000	Weak transcription	Right Atrium	heart
26	chr12:48139400-48147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:48139600-48141800	Enhancers	Primary B cells from cord blood	blood
28	chr12:48139600-48144200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:48139600-48145200	Strong transcription	Lung	lung
30	chr12:48139800-48143600	Strong transcription	Right Ventricle	heart
31	chr12:48139800-48144000	Strong transcription	Ovary	ovary
32	chr12:48139800-48144200	Strong transcription	Adipose Nuclei	Adipose
33	chr12:48139800-48146600	Weak transcription	Fetal Lung	lung
34	chr12:48139800-48146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:48140000-48143800	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:48140000-48145400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr12:48140200-48141800	Genic enhancers	Spleen	Spleen
38	chr12:48140200-48142200	Strong transcription	Left Ventricle	heart
39	chr12:48140200-48143400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:48140200-48144600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:48140200-48145200	Strong transcription	Brain Hippocampus Middle	brain
42	chr12:48140200-48145400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr12:48140200-48145600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:48140200-48145600	Strong transcription	Brain Substantia Nigra	brain
45	chr12:48140200-48146200	Strong transcription	Fetal Stomach	stomach
46	chr12:48140200-48146800	Weak transcription	Fetal Heart	heart
47	chr12:48140400-48142000	Strong transcription	NHEK	skin
48	chr12:48140400-48144200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:48140400-48144200	Strong transcription	Placenta	Placenta
50	chr12:48140400-48144600	Strong transcription	Esophagus	oesophagus

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