Variant report

Variant	rs17117921
Chromosome Location	chr12:56113485-56113486
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:5)
LncRNA
region (count:0)
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	RCOR1	chr12:56113463-56116004	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:56113243-56124503	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56099897..56102707-chr12:56112712..56115453,3	K562	blood:
2	chr12:56073967..56077119-chr12:56108776..56115360,8	MCF-7	breast:
3	chr12:56112120..56114642-chr12:56221264..56223101,2	K562	blood:
4	chr12:56112563..56114483-chr12:56136186..56139060,2	K562	blood:
5	chr12:56097454..56102551-chr12:56112712..56115569,4	K562	blood:

No data

Variant related genes	Relation type
ITGA7	TF binding region
RDH5	TF binding region
ENSG00000135424	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000170439	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56818653	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 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	chr12:56109000-56115600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr12:56110600-56113600	Flanking Active TSS	HSMMtube	muscle
3	chr12:56110800-56114600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:56111000-56114200	Enhancers	Psoas Muscle	Psoas
5	chr12:56111000-56114600	Flanking Active TSS	HSMM	muscle
6	chr12:56111200-56113800	Enhancers	HepG2	liver
7	chr12:56111200-56114200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:56111200-56114200	Genic enhancers	Fetal Intestine Small	intestine
9	chr12:56111200-56114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:56111200-56115000	Enhancers	Esophagus	oesophagus
11	chr12:56111200-56115600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr12:56111200-56115800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:56111200-56115800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:56111200-56115800	Enhancers	Right Atrium	heart
15	chr12:56111200-56120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:56111400-56114200	Enhancers	Liver	Liver
17	chr12:56111400-56115400	Enhancers	Left Ventricle	heart
18	chr12:56111600-56113800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:56111600-56114000	Genic enhancers	Fetal Thymus	thymus
20	chr12:56111600-56114200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr12:56111600-56115800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:56111600-56115800	Enhancers	HMEC	breast
23	chr12:56111600-56118400	Strong transcription	Thymus	Thymus
24	chr12:56111800-56113800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:56111800-56114200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:56111800-56114200	Genic enhancers	Fetal Stomach	stomach
27	chr12:56111800-56114200	Genic enhancers	Spleen	Spleen
28	chr12:56111800-56114400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:56111800-56114800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:56111800-56115000	Weak transcription	K562	blood
31	chr12:56112000-56114400	Enhancers	Colonic Mucosa	Colon
32	chr12:56112000-56115600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:56112000-56117800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:56112200-56114000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:56112200-56114000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:56112200-56114400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:56112200-56115200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr12:56112200-56116600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:56112200-56118000	Weak transcription	Fetal Lung	lung
40	chr12:56112400-56113600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:56112400-56113600	Enhancers	NHDF-Ad	bronchial
42	chr12:56112400-56113600	Weak transcription	NHEK	skin
43	chr12:56112400-56113800	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr12:56112400-56114200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:56112400-56114200	Weak transcription	HUVEC	blood vessel
46	chr12:56112400-56114400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:56112400-56114600	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:56112400-56114800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:56112400-56115400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr12:56112400-56115400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links