Variant report

Variant	rs1338466
Chromosome Location	chr6:45952118-45952119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10484841	0.88[MEX][hapmap]
rs2021685	0.84[ASN][1000 genomes]
rs2021686	0.87[ASN][1000 genomes]
rs3777601	0.82[MEX][hapmap]
rs9463163	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1338466	TRIM41	trans	parietal	SCAN
rs1338466	RHAG	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45938600-45953200	Weak transcription	Lung	lung
2	chr6:45943400-45952600	Weak transcription	Placenta	Placenta
3	chr6:45946600-45954800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr6:45946800-45952600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:45949400-45954600	Weak transcription	Fetal Kidney	kidney
6	chr6:45950600-45960200	Enhancers	Psoas Muscle	Psoas
7	chr6:45950800-45953400	Genic enhancers	Left Ventricle	heart
8	chr6:45951000-45952400	Weak transcription	Fetal Heart	heart
9	chr6:45951000-45952400	Weak transcription	Right Ventricle	heart
10	chr6:45951000-45955200	Enhancers	Right Atrium	heart
11	chr6:45951200-45954800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:45951400-45953400	Strong transcription	Fetal Intestine Large	intestine
13	chr6:45951400-45954000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:45951400-45954200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:45951400-45956400	Weak transcription	Small Intestine	intestine
16	chr6:45951600-45954200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:45952000-45954000	Strong transcription	Fetal Intestine Small	intestine

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