Variant report

Variant	rs11682848
Chromosome Location	chr2:234910928-234910929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10929320	1.00[YRI][hapmap]
rs11563009	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17863818	1.00[YRI][hapmap]
rs17869073	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs601885	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs664373	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7570755	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11682848	PDE6D	cis	parietal	SCAN
rs11682848	UGT1A1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234898600-234912400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:234903000-234912400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234904800-234911400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:234906000-234911400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:234906800-234912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:234908400-234912600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:234909000-234911200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:234909000-234911200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:234909000-234911200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:234909000-234911200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:234909000-234911600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:234909200-234911200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:234909200-234911200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:234909400-234911000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr2:234909400-234911400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:234909600-234912600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:234909600-234919000	Strong transcription	Liver	Liver
18	chr2:234910400-234911200	Enhancers	Primary T killer naive cells fromperipheralblood	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