Variant report

Variant	rs235623
Chromosome Location	chr12:47058843-47058844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46660431..46663330-chr12:47057064..47059822,2	MCF-7	breast:
2	chr12:46763815..46766658-chr12:47056305..47059376,3	K562	blood:
3	chr12:46884995..46887012-chr12:47057652..47060520,3	MCF-7	breast:
4	chr12:46772586..46775083-chr12:47057146..47059153,2	MCF-7	breast:
5	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
6	chr12:46902819..46905512-chr12:47057420..47060601,3	MCF-7	breast:
7	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
8	chr12:47054064..47055917-chr12:47057458..47059164,2	K562	blood:
9	chr12:47058195..47060784-chr12:47071093..47073736,2	MCF-7	breast:
10	chr12:47057391..47059598-chr12:47067788..47069544,2	MCF-7	breast:
11	chr12:46775360..46780494-chr12:47054865..47060216,9	MCF-7	breast:
12	chr12:46901974..46903711-chr12:47058185..47060406,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11183554	0.87[AFR][1000 genomes]
rs12316011	0.80[YRI][hapmap]
rs1946173	0.80[YRI][hapmap]
rs235620	0.80[YRI][hapmap]
rs2543342	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:47053400-47062400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:47054400-47059400	Weak transcription	Psoas Muscle	Psoas
7	chr12:47055400-47059600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:47055600-47059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:47055600-47059400	Weak transcription	Fetal Kidney	kidney
10	chr12:47056000-47069000	Weak transcription	Esophagus	oesophagus
11	chr12:47056800-47060200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:47057000-47059600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:47057000-47059800	Enhancers	NHLF	lung
14	chr12:47057000-47059800	Enhancers	Osteobl	bone
15	chr12:47057000-47060200	Enhancers	HUVEC	blood vessel
16	chr12:47058000-47059000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:47058000-47059600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:47058000-47059600	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:47058000-47059600	Enhancers	HSMM	muscle
20	chr12:47058000-47059600	Enhancers	HSMMtube	muscle
21	chr12:47058000-47059600	Enhancers	NH-A	brain
22	chr12:47058200-47059000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr12:47058200-47059000	Flanking Active TSS	HepG2	liver
24	chr12:47058200-47059200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr12:47058200-47059400	Flanking Active TSS	NHEK	skin
26	chr12:47058200-47059600	Flanking Active TSS	A549	lung
27	chr12:47058200-47059600	Enhancers	K562	blood
28	chr12:47058200-47059800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr12:47058400-47059000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:47058400-47059000	Flanking Active TSS	HMEC	breast
31	chr12:47058400-47059000	Flanking Active TSS	NHDF-Ad	bronchial
32	chr12:47058400-47059200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr12:47058400-47059200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:47058400-47059400	Enhancers	GM12878-XiMat	blood
35	chr12:47058400-47059600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:47058600-47059000	Enhancers	Primary B cells from cord blood	blood
37	chr12:47058600-47059000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:47058600-47059000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:47058600-47059000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:47058600-47059000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:47058600-47059200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:47058600-47059200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr12:47058600-47059400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr12:47058600-47059400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr12:47058600-47059600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr12:47058600-47059600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:47058600-47059600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:47058800-47059000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr12:47058800-47059000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:47058800-47059600	Flanking Active TSS	Hela-S3	cervix

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