Variant report

Variant	rs28404612
Chromosome Location	chr4:53879402-53879403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53875015..53876837-chr4:53878881..53881020,2	K562	blood:
2	chr4:53872595..53874436-chr4:53878591..53881350,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10013152	0.81[ASN][1000 genomes]
rs10024057	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11941906	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1384696	0.81[ASN][1000 genomes]
rs17082301	0.81[ASN][1000 genomes]
rs2062185	0.81[ASN][1000 genomes]
rs2062186	0.81[ASN][1000 genomes]
rs28592856	0.81[ASN][1000 genomes]
rs28713187	0.81[ASN][1000 genomes]
rs3912335	0.81[ASN][1000 genomes]
rs4419529	0.81[ASN][1000 genomes]
rs4864712	0.81[ASN][1000 genomes]
rs4864713	0.81[ASN][1000 genomes]
rs4864714	0.81[ASN][1000 genomes]
rs4864715	0.81[ASN][1000 genomes]
rs6822707	0.81[ASN][1000 genomes]
rs6825075	0.81[ASN][1000 genomes]
rs7658716	0.84[ASN][1000 genomes]
rs7671836	0.81[ASN][1000 genomes]
rs7673017	0.81[ASN][1000 genomes]
rs7694940	0.81[ASN][1000 genomes]
rs9312635	0.81[ASN][1000 genomes]
rs9999433	0.81[ASN][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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv508280	chr4:53825060-53907661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53870800-53880200	Weak transcription	Esophagus	oesophagus
2	chr4:53873200-53880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:53873400-53886800	Weak transcription	Left Ventricle	heart
4	chr4:53874000-53879800	Enhancers	Fetal Lung	lung
5	chr4:53874000-53882200	Enhancers	Fetal Kidney	kidney
6	chr4:53874600-53885000	Weak transcription	Spleen	Spleen
7	chr4:53875600-53881400	Weak transcription	HepG2	liver
8	chr4:53875800-53882200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr4:53876000-53879600	Enhancers	Colon Smooth Muscle	Colon
10	chr4:53876000-53879600	Enhancers	Fetal Thymus	thymus
11	chr4:53876000-53885800	Weak transcription	Small Intestine	intestine
12	chr4:53876200-53883000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:53876400-53882600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:53876600-53880800	Enhancers	Adipose Nuclei	Adipose
15	chr4:53876800-53884600	Weak transcription	Liver	Liver
16	chr4:53877400-53879600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:53877400-53879600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:53877400-53880600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:53877600-53879600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:53877600-53879800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:53877600-53880400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr4:53877600-53881600	Enhancers	Fetal Muscle Leg	muscle
23	chr4:53877600-53881800	Enhancers	Fetal Intestine Large	intestine
24	chr4:53877800-53879600	Enhancers	Pancreas	Pancrea
25	chr4:53877800-53879600	Enhancers	HUVEC	blood vessel
26	chr4:53877800-53879800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:53877800-53880200	Enhancers	Fetal Stomach	stomach
28	chr4:53877800-53880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:53877800-53880600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:53878000-53879600	Enhancers	NH-A	brain
31	chr4:53878200-53881800	Enhancers	Fetal Intestine Small	intestine
32	chr4:53878400-53879600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:53878400-53880200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:53878400-53880400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:53878400-53882800	Enhancers	NHLF	lung
36	chr4:53878400-53888000	Weak transcription	Right Atrium	heart
37	chr4:53878600-53880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:53878800-53879600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr4:53878800-53879600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr4:53878800-53880400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr4:53878800-53886200	Weak transcription	Psoas Muscle	Psoas
42	chr4:53879000-53879600	Enhancers	Ovary	ovary
43	chr4:53879000-53880000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:53879200-53879600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr4:53879200-53879600	Flanking Active TSS	GM12878-XiMat	blood
46	chr4:53879200-53880400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr4:53879200-53883000	Enhancers	Osteobl	bone
48	chr4:53879200-53885000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:53879200-53885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:53879400-53879800	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links