Variant report

Variant	rs2042839
Chromosome Location	chr2:231443567-231443568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11689558	1.00[YRI][hapmap]
rs1564322	1.00[JPT][hapmap]
rs2042840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194773	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194775	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194776	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194778	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194779	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194780	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194781	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194782	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194783	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875953	chr2:231415189-231457819	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875955	chr2:231440555-231500805	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763113	chr2:231441828-231445303	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2042839	SCARNA6	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231439800-231443800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr2:231441000-231447200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:231442000-231443600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:231442600-231445000	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:231442800-231444000	Enhancers	Primary B cells from cord blood	blood
6	chr2:231442800-231444200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:231443200-231443600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr2:231443200-231444000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:231443400-231443600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr2:231443400-231451000	Weak transcription	Primary T cells from cord blood	blood
11	chr2:231443400-231453800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:231443400-231454400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:231443400-231454600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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