Variant report

Variant	rs56910713
Chromosome Location	chr12:123736893-123736894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123735839-123737024	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123736694-123736906	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123464634..123466197-chr12:123735539..123737109,2	MCF-7	breast:
2	chr12:123715622..123719446-chr12:123735072..123738647,4	K562	blood:
3	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
4	chr12:123733810..123737382-chr12:123754694..123758405,4	MCF-7	breast:
5	chr12:123735647..123738456-chr12:123742871..123745926,3	K562	blood:
6	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:
7	chr12:123735701..123738592-chr12:123744837..123746422,2	MCF-7	breast:
8	chr12:123735336..123737474-chr12:123737604..123739915,2	MCF-7	breast:
9	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK2AP1-1	chr12:123736789-123737089	ENSG00000235423.4
2	lnc-CDK2AP1-1	chr12:123736577-123737089	ENSG00000235423.3
3	lnc-CDK2AP1-1	chr12:123736789-123737089	ENSG00000235423.3

No data

Variant related genes	Relation type
C12orf65	TF binding region
ENSG00000235423	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs59708426	0.85[AMR][1000 genomes]
rs7299155	0.85[AMR][1000 genomes]
rs73417342	0.85[AMR][1000 genomes]
rs73417343	0.85[AMR][1000 genomes]
rs73417346	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73417348	0.86[AFR][1000 genomes];0.85[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
2	chr12:123719600-123738400	Weak transcription	NH-A	brain
3	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
4	chr12:123725200-123738000	Weak transcription	HSMM	muscle
5	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:123727400-123738000	Weak transcription	NHDF-Ad	bronchial
7	chr12:123727400-123738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:123727600-123738000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:123727600-123738000	Weak transcription	HUVEC	blood vessel
10	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:123727800-123738200	Weak transcription	Fetal Heart	heart
12	chr12:123732000-123738200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:123732800-123737000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:123733400-123738000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:123733400-123738000	Weak transcription	Primary B cells from cord blood	blood
16	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:123733800-123738000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:123734000-123737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:123734000-123738400	Weak transcription	Osteobl	bone
20	chr12:123734200-123737800	Weak transcription	GM12878-XiMat	blood
21	chr12:123734200-123738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:123734400-123738400	Weak transcription	Aorta	Aorta
23	chr12:123734400-123738600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:123734800-123737000	Enhancers	Esophagus	oesophagus
26	chr12:123735000-123737000	Enhancers	Brain Substantia Nigra	brain
27	chr12:123735000-123737000	Genic enhancers	Fetal Intestine Small	intestine
28	chr12:123735000-123737000	Enhancers	Psoas Muscle	Psoas
29	chr12:123735000-123737200	Enhancers	Brain Anterior Caudate	brain
30	chr12:123735000-123737200	Genic enhancers	Fetal Brain Female	brain
31	chr12:123735000-123737200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:123735000-123737200	Enhancers	Stomach Mucosa	stomach
33	chr12:123735000-123738000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:123735000-123738600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:123735000-123740400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:123735200-123737000	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:123735200-123737000	Genic enhancers	Brain Germinal Matrix	brain
38	chr12:123735200-123737000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:123735200-123737000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr12:123735200-123738800	Enhancers	Brain Cingulate Gyrus	brain
41	chr12:123735200-123739600	Enhancers	Fetal Brain Male	brain
42	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
43	chr12:123735400-123737000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:123735400-123738000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:123735400-123738000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:123735400-123738000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:123735400-123738000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:123735400-123739200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:123735600-123737800	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links