Variant report

Variant	rs4865009
Chromosome Location	chr4:56414723-56414724
allele	G/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	MXI1	chr4:56410957-56414953	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56414679..56416401-chr4:56437993..56440947,2	K562	blood:

Variant related genes	Relation type
CLOCK	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13144358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1844218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2130034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2130037	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2175641	1.00[AMR][1000 genomes]
rs2412651	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2459221	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3103344	1.00[AMR][1000 genomes]
rs556776	1.00[AMR][1000 genomes]
rs977061	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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56413200-56415000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56413800-56414800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:56413800-56414800	Enhancers	Stomach Mucosa	stomach
4	chr4:56413800-56415000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr4:56414000-56414800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:56414000-56414800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr4:56414000-56414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:56414000-56414800	Flanking Active TSS	HepG2	liver
9	chr4:56414000-56414800	Enhancers	K562	blood
10	chr4:56414000-56415600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:56414000-56416800	Enhancers	Fetal Intestine Small	intestine
12	chr4:56414000-56419200	Weak transcription	Adipose Nuclei	Adipose
13	chr4:56414000-56419200	Weak transcription	Right Atrium	heart
14	chr4:56414000-56419400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:56414200-56414800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:56414200-56414800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr4:56414200-56414800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:56414200-56414800	Enhancers	Fetal Heart	heart
19	chr4:56414200-56414800	Enhancers	Fetal Lung	lung
20	chr4:56414200-56415000	Enhancers	Fetal Stomach	stomach
21	chr4:56414200-56415200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr4:56414200-56415800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:56414200-56415800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:56414200-56415800	Enhancers	Fetal Intestine Large	intestine
25	chr4:56414200-56417600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:56414200-56417600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:56414200-56420400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:56414400-56414800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:56414400-56414800	Enhancers	Fetal Brain Female	brain
30	chr4:56414400-56415000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:56414400-56415000	Enhancers	Fetal Kidney	kidney
32	chr4:56414400-56416200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:56414400-56416200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:56414400-56416200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:56414400-56416800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:56414400-56417200	Enhancers	HMEC	breast
37	chr4:56414400-56417600	Enhancers	NHEK	skin
38	chr4:56414400-56418800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:56414400-56419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:56414400-56419200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:56414400-56419200	Weak transcription	GM12878-XiMat	blood
42	chr4:56414600-56414800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:56414600-56414800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:56414600-56414800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr4:56414600-56414800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:56414600-56414800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:56414600-56414800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:56414600-56414800	Active TSS	Brain Angular Gyrus	brain
49	chr4:56414600-56414800	Enhancers	Brain Germinal Matrix	brain
50	chr4:56414600-56414800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links