Variant report

Variant	rs28566610
Chromosome Location	chr4:120534922-120534923
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120532371..120535379-chr4:120540193..120542602,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10012485	0.87[EUR][1000 genomes]
rs10021460	0.85[EUR][1000 genomes]
rs10022664	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518335	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12502511	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503853	0.84[EUR][1000 genomes]
rs12642735	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12646525	0.85[EUR][1000 genomes]
rs12648259	0.85[EUR][1000 genomes]
rs13115778	0.87[EUR][1000 genomes]
rs1987179	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248236	0.84[EUR][1000 genomes]
rs2389863	0.86[EUR][1000 genomes]
rs2389864	0.87[EUR][1000 genomes]
rs2389866	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2389869	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2622499	0.84[EUR][1000 genomes]
rs2622500	0.84[EUR][1000 genomes]
rs28382361	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28412979	0.87[EUR][1000 genomes]
rs28540362	0.84[EUR][1000 genomes]
rs28564258	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28625289	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28650385	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2892867	0.87[EUR][1000 genomes]
rs2928993	0.84[EUR][1000 genomes]
rs2928994	0.81[EUR][1000 genomes]
rs3733526	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3756154	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3756157	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4337718	0.81[EUR][1000 genomes]
rs4597811	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4626181	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4833622	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834784	0.85[EUR][1000 genomes]
rs6534146	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6534147	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822275	0.83[EUR][1000 genomes]
rs6834347	0.85[EUR][1000 genomes]
rs6842674	0.87[EUR][1000 genomes]
rs6847164	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7659250	0.87[EUR][1000 genomes]
rs7670921	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7672961	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681796	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7684899	0.87[EUR][1000 genomes]
rs9998919	0.87[EUR][1000 genomes];0.81[ASN][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
3	chr4:120517000-120536600	Weak transcription	Ovary	ovary
4	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:120525800-120538800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:120526400-120544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:120526600-120535400	Weak transcription	Fetal Brain Male	brain
12	chr4:120527400-120536400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:120528800-120539000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:120528800-120540200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:120528800-120543000	Weak transcription	Pancreas	Pancrea
19	chr4:120528800-120544200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
21	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:120532000-120536200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:120532200-120535600	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:120532200-120536000	Weak transcription	Aorta	Aorta
25	chr4:120532400-120536600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:120532400-120547600	Weak transcription	Lung	lung
27	chr4:120533000-120544200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:120533600-120535800	Weak transcription	Fetal Lung	lung
29	chr4:120533600-120539200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:120533600-120547400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:120534000-120536400	Weak transcription	NHLF	lung
32	chr4:120534000-120536600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:120534000-120547400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:120534800-120536600	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links