Variant report

Variant	rs58578647
Chromosome Location	chr4:56419315-56419316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56367962..56369709-chr4:56418352..56420370,2	K562	blood:
2	chr4:56410487..56414437-chr4:56418124..56420516,3	MCF-7	breast:
3	chr4:56417353..56420509-chr4:56422017..56425975,3	K562	blood:
4	chr4:56410648..56414304-chr4:56416638..56420885,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1047343	1.00[AMR][1000 genomes]
rs10517345	1.00[AMR][1000 genomes]
rs1552522	1.00[AMR][1000 genomes]
rs17085783	1.00[AMR][1000 genomes]
rs17085803	1.00[AMR][1000 genomes]
rs17085857	1.00[AMR][1000 genomes]
rs17085864	1.00[AMR][1000 genomes]
rs17085882	1.00[AMR][1000 genomes]
rs17085885	1.00[AMR][1000 genomes]
rs2412650	1.00[AMR][1000 genomes]
rs34028624	1.00[AMR][1000 genomes]
rs34822003	1.00[AMR][1000 genomes]
rs73151822	1.00[AMR][1000 genomes]
rs73151893	1.00[AMR][1000 genomes]
rs73153621	1.00[AMR][1000 genomes]
rs73153661	1.00[AMR][1000 genomes]
rs73153688	1.00[AMR][1000 genomes]
rs73816271	1.00[AMR][1000 genomes]
rs73816274	1.00[AMR][1000 genomes]
rs7657206	1.00[AMR][1000 genomes]
rs7659053	1.00[AMR][1000 genomes]
rs7661096	1.00[AMR][1000 genomes]
rs7662129	1.00[AMR][1000 genomes]
rs7663749	1.00[AMR][1000 genomes]
rs7686016	1.00[AMR][1000 genomes]
rs7696080	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56414000-56419400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:56414200-56420400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:56414600-56419800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:56414800-56419600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:56414800-56419600	Weak transcription	Fetal Lung	lung
6	chr4:56414800-56419800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:56414800-56419800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:56414800-56420000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:56414800-56420000	Weak transcription	Fetal Brain Female	brain
10	chr4:56415000-56419400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:56415000-56419600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:56415000-56419600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:56415000-56419800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:56415000-56419800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:56415000-56419800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:56416400-56419400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:56416400-56420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:56416800-56419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:56416800-56419400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:56416800-56419400	Weak transcription	HSMM	muscle
21	chr4:56416800-56419400	Weak transcription	NHDF-Ad	bronchial
22	chr4:56416800-56420600	Weak transcription	Fetal Intestine Large	intestine
23	chr4:56416800-56425600	Weak transcription	K562	blood
24	chr4:56417000-56419600	Weak transcription	NH-A	brain
25	chr4:56417600-56419400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:56417600-56419600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:56417600-56420000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:56417600-56420000	Weak transcription	NHEK	skin
29	chr4:56418800-56431800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:56419000-56419400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:56419000-56419400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:56419000-56419400	Enhancers	Aorta	Aorta
33	chr4:56419000-56419400	Enhancers	Fetal Muscle Leg	muscle
34	chr4:56419000-56419400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:56419000-56419600	Enhancers	Primary B cells from peripheral blood	blood
36	chr4:56419000-56419800	Active TSS	Duodenum Mucosa	Duodenum
37	chr4:56419200-56419400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:56419200-56419400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr4:56419200-56419400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:56419200-56419400	Enhancers	Adipose Nuclei	Adipose
41	chr4:56419200-56419400	Enhancers	Brain Hippocampus Middle	brain
42	chr4:56419200-56419400	Enhancers	Colon Smooth Muscle	Colon
43	chr4:56419200-56419400	Enhancers	Psoas Muscle	Psoas
44	chr4:56419200-56419400	Flanking Active TSS	HepG2	liver
45	chr4:56419200-56419600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:56419200-56419600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:56419200-56419800	Active TSS	Rectal Smooth Muscle	rectum
48	chr4:56419200-56419800	Active TSS	GM12878-XiMat	blood
49	chr4:56419200-56420000	Active TSS	Right Atrium	heart
50	chr4:56419200-56420000	Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links