Variant report

Variant	rs7560985
Chromosome Location	chr2:168146167-168146168
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10193480	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10497323	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12611980	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12612028	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1357598	0.89[EUR][1000 genomes]
rs1564384	0.81[ASN][1000 genomes]
rs1842233	0.82[ASN][1000 genomes]
rs2177440	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2204279	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4315485	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60477253	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60988732	0.92[EUR][1000 genomes]
rs61036436	0.92[EUR][1000 genomes]
rs6708386	0.81[ASN][1000 genomes]
rs73029721	0.81[EUR][1000 genomes]
rs7564986	0.81[EUR][1000 genomes]
rs7603500	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7605309	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9784125	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv875377	chr2:168084857-168203116	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv875378	chr2:168107491-168297961	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3364733	chr2:168109919-168302141	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7560985	SCN9A	cis	brain	BrainEAC

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:168144000-168148600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:168144400-168148000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:168144600-168148000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:168144600-168148800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:168144800-168148000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:168144800-168148200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:168145000-168148000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:168145600-168148000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:168145800-168147800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:168145800-168148000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:168145800-168148200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links