Variant report

Variant	rs17078346
Chromosome Location	chr3:45845748-45845749
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12721497	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13081482	1.00[CEU][hapmap]
rs17078348	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078401	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2191032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34326463	0.81[EUR][1000 genomes]
rs4683145	0.86[ASN][1000 genomes]
rs72893671	0.86[EUR][1000 genomes]
rs9856760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17078346	ALS2CL	cis	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45838400-45860000	Weak transcription	Gastric	stomach
2	chr3:45841000-45847600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:45842000-45849400	Strong transcription	Dnd41	blood
4	chr3:45842400-45857400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:45842400-45859200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:45842400-45859800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:45842600-45854400	Weak transcription	Fetal Intestine Large	intestine
8	chr3:45843000-45846800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:45843200-45846400	Strong transcription	Thymus	Thymus
10	chr3:45843800-45849800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:45843800-45856400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:45844000-45857400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:45844400-45846600	Strong transcription	Fetal Thymus	thymus
14	chr3:45845400-45853600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:45845400-45858800	Weak transcription	Brain Germinal Matrix	brain

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