Variant report

Variant	rs3773506
Chromosome Location	chr3:142431000-142431001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1403725	0.90[ASW][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1523516	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16852615	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2883546	0.82[ASN][1000 genomes]
rs4541445	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57139089	0.82[ASN][1000 genomes]
rs6784134	0.82[ASN][1000 genomes]
rs73000186	0.92[EUR][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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv520533	chr3:142417070-142440299	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes	21490949	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3773506	PLS1	cis	lymphoblastoid	seeQTL
rs3773506	TRPC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:142425800-142431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:142426200-142435000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:142429400-142442400	Weak transcription	NH-A	brain
7	chr3:142429600-142442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:142430200-142431600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr3:142430400-142431000	Strong transcription	Liver	Liver
10	chr3:142430600-142431800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr3:142430600-142433200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:142431000-142433400	Weak transcription	Liver	Liver

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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

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