Variant report

Variant	rs57560943
Chromosome Location	chr2:54599889-54599890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10167922	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10179958	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10194310	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11675478	0.84[ASN][1000 genomes]
rs11685447	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13405819	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17268437	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2280717	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28524007	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57047379	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72917496	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72917498	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54587600-54606200	Weak transcription	Fetal Kidney	kidney
2	chr2:54596800-54600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:54597200-54601400	Enhancers	Adipose Nuclei	Adipose
4	chr2:54597600-54600000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:54597800-54600600	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:54597800-54600600	Enhancers	Placenta	Placenta
7	chr2:54597800-54600800	Enhancers	Right Atrium	heart
8	chr2:54597800-54601000	Enhancers	Fetal Muscle Leg	muscle
9	chr2:54597800-54601200	Enhancers	Right Ventricle	heart
10	chr2:54597800-54601400	Enhancers	Left Ventricle	heart
11	chr2:54598000-54600000	Enhancers	Fetal Heart	heart
12	chr2:54598400-54601000	Enhancers	Psoas Muscle	Psoas
13	chr2:54598400-54602000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:54598600-54600200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:54598600-54600200	Enhancers	HSMM	muscle
16	chr2:54598800-54611000	Weak transcription	Brain Substantia Nigra	brain
17	chr2:54599000-54600200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:54599000-54601200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:54599000-54601800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:54599000-54601800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:54599000-54605000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:54599000-54607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:54599000-54611800	Weak transcription	Ovary	ovary
24	chr2:54599000-54614800	Weak transcription	Pancreas	Pancrea
25	chr2:54599200-54600000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:54599200-54601200	Weak transcription	Fetal Lung	lung
27	chr2:54599200-54611200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:54599600-54601000	Enhancers	Lung	lung
29	chr2:54599600-54601400	Enhancers	HSMMtube	muscle
30	chr2:54599600-54607600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:54599800-54600000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:54599800-54600800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links