Variant report

Variant	rs10059539
Chromosome Location	chr5:7828404-7828405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10475396	0.89[ASN][1000 genomes]
rs10475397	0.83[ASN][1000 genomes]
rs326187	0.87[ASN][1000 genomes]
rs326189	0.83[ASN][1000 genomes]
rs326190	0.83[ASN][1000 genomes]
rs34384504	0.89[ASN][1000 genomes]
rs35949686	0.89[ASN][1000 genomes]
rs6878924	0.89[ASN][1000 genomes]
rs6878965	0.87[ASN][1000 genomes]
rs6883562	0.89[ASN][1000 genomes]
rs72001	0.87[ASN][1000 genomes]
rs9313205	0.93[ASN][1000 genomes]
rs9313206	0.89[ASN][1000 genomes]
rs9313207	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv461927	chr5:7757812-7854289	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv597004	chr5:7757812-7854289	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr5:7816800-7828800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:7819200-7829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:7820000-7830200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:7822000-7828600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:7822000-7829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:7825600-7828800	Weak transcription	Pancreas	Pancrea
7	chr5:7825600-7829200	Weak transcription	Gastric	stomach
8	chr5:7825600-7830200	Weak transcription	Aorta	Aorta
9	chr5:7827200-7828600	Weak transcription	Brain Substantia Nigra	brain
10	chr5:7827200-7828800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:7827200-7828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:7827200-7829000	Weak transcription	Fetal Intestine Small	intestine
13	chr5:7827400-7828800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:7827400-7828800	Enhancers	Brain Cingulate Gyrus	brain
15	chr5:7827400-7829200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:7827400-7829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:7827400-7829200	Enhancers	Brain Germinal Matrix	brain
18	chr5:7827400-7829200	Enhancers	Brain Hippocampus Middle	brain
19	chr5:7827600-7829400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:7827600-7829400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:7827600-7829400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:7827600-7829400	Weak transcription	Ovary	ovary
23	chr5:7827600-7829800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:7827600-7830200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:7827600-7830600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:7827600-7831000	Weak transcription	Fetal Stomach	stomach
27	chr5:7827600-7833600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:7827600-7834000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:7827800-7830000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:7828000-7828800	Enhancers	Fetal Heart	heart
31	chr5:7828000-7829000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:7828200-7829200	Enhancers	Brain Anterior Caudate	brain
33	chr5:7828200-7833600	Weak transcription	Fetal Brain Male	brain
34	chr5:7828400-7828600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:7828400-7839000	Weak transcription	Fetal Brain Female	brain

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