Variant report

Variant	rs6594684
Chromosome Location	chr5:112461911-112461912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:112460765-112462145	SK-N-SH	brain:	n/a	chr5:112461052-112461062 chr5:112460979-112460993

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112455253..112458185-chr5:112461323..112464102,2	MCF-7	breast:
2	chr5:112459886..112461931-chr5:112462862..112464863,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11952087	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35555142	0.83[EUR][1000 genomes]
rs4235792	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4259163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4454046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4458560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527591	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4582268	1.00[EUR][1000 genomes]
rs4705541	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705781	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60681208	0.83[EUR][1000 genomes]
rs62373350	0.83[EUR][1000 genomes]
rs62373352	0.83[EUR][1000 genomes]
rs62374676	0.83[EUR][1000 genomes]
rs62374682	0.83[EUR][1000 genomes]
rs62374707	0.83[EUR][1000 genomes]
rs62374708	1.00[EUR][1000 genomes]
rs62374709	1.00[EUR][1000 genomes]
rs62374711	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594688	0.92[AFR][1000 genomes]
rs6594689	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6872711	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237129	1.00[EUR][1000 genomes]
rs7703001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
2	chr5:112455000-112462200	Enhancers	Fetal Heart	heart
3	chr5:112456600-112467200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:112457400-112462000	Enhancers	Adipose Nuclei	Adipose
5	chr5:112458400-112474200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:112458600-112474000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:112458600-112477000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112458800-112476600	Weak transcription	NHEK	skin
9	chr5:112459200-112462000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:112459400-112468400	Weak transcription	NHDF-Ad	bronchial
11	chr5:112459600-112462200	Enhancers	Liver	Liver
12	chr5:112459600-112462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:112459800-112462600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:112460200-112462000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:112460600-112462400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:112460600-112462600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:112460600-112463600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:112460600-112465000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:112460800-112462400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:112460800-112464600	Weak transcription	Psoas Muscle	Psoas
21	chr5:112460800-112466800	Weak transcription	Fetal Brain Male	brain
22	chr5:112460800-112467400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:112461000-112466600	Weak transcription	Right Atrium	heart
24	chr5:112461200-112469400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:112461400-112466200	Weak transcription	Left Ventricle	heart
26	chr5:112461400-112466600	Weak transcription	Right Ventricle	heart
27	chr5:112461400-112468400	Weak transcription	Ovary	ovary
28	chr5:112461400-112476800	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:112461600-112462000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:112461600-112462200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:112461600-112462200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:112461600-112464000	Weak transcription	Fetal Brain Female	brain
33	chr5:112461800-112462200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:112461800-112462400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:112461800-112463600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:112461800-112463800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:112461800-112476200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links