Variant report

Variant	rs55904344
Chromosome Location	chr3:42794333-42794334
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42792752..42794704-chr3:42802207..42805435,3	K562	blood:
2	chr3:42623610..42625161-chr3:42793452..42795180,2	K562	blood:
3	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10461012	0.93[EUR][1000 genomes]
rs10865920	0.96[EUR][1000 genomes]
rs10865921	0.96[EUR][1000 genomes]
rs10865923	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11129969	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129970	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709054	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713172	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915803	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17074778	0.96[EUR][1000 genomes]
rs17238314	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238798	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2240861	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34110933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682856	0.90[EUR][1000 genomes]
rs55884426	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59478814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59713146	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60049195	0.96[EUR][1000 genomes]
rs60176972	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62246603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246606	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246629	0.81[EUR][1000 genomes]
rs62246635	0.89[EUR][1000 genomes]
rs62250113	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62250114	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442057	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72865716	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9836162	0.94[EUR][1000 genomes]
rs9837412	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9838388	0.86[EUR][1000 genomes]
rs9880635	0.82[EUR][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
4	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:42788600-42796000	Weak transcription	Adipose Nuclei	Adipose
6	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:42788800-42794400	Weak transcription	Gastric	stomach
8	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
9	chr3:42789000-42795200	Weak transcription	Aorta	Aorta
10	chr3:42789000-42795600	Weak transcription	Fetal Brain Female	brain
11	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:42791400-42795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:42791400-42797200	Weak transcription	Fetal Heart	heart
15	chr3:42791600-42797400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
17	chr3:42791800-42797000	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:42791800-42797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:42791800-42797200	Weak transcription	Brain Anterior Caudate	brain
20	chr3:42791800-42797800	Weak transcription	Pancreas	Pancrea
21	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
22	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:42792000-42795600	Weak transcription	HepG2	liver
24	chr3:42792000-42797200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:42792000-42797200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:42792000-42797200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:42793600-42794600	Weak transcription	Placenta	Placenta
29	chr3:42793600-42794800	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:42793600-42797000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:42793600-42797200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:42793600-42797400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:42793600-42802600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:42793600-42802600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:42793600-42811000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links