Variant report

Variant	rs10076280
Chromosome Location	chr5:2164846-2164847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10045167	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056093	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10056218	0.94[ASN][1000 genomes]
rs10056351	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062483	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065589	0.94[ASN][1000 genomes]
rs10068467	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068538	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069270	0.94[ASN][1000 genomes]
rs10072352	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10076073	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076279	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133929	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133930	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11133931	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133932	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746469	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12652492	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654394	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655177	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16903364	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57251700	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863477	0.99[ASN][1000 genomes]
rs72710663	0.93[ASN][1000 genomes]
rs72710668	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72710682	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv880972	chr5:2146761-2190572	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv880947	chr5:2146761-2251313	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881232	chr5:2150273-2213762	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv881517	chr5:2159490-2186956	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv880859	chr5:2159490-2190572	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv880789	chr5:2159490-2213762	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10076280	C5orf55	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2158000-2171000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:2163200-2166200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr5:2163400-2166200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:2163600-2165000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:2163800-2165200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:2163800-2165400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr5:2163800-2165600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:2163800-2165800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:2164000-2165000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr5:2164000-2166200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
11	chr5:2164200-2165200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:2164400-2165800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:2164600-2165000	Bivalent Enhancer	Fetal Stomach	stomach
14	chr5:2164600-2165400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:2164800-2165800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links