Variant report

Variant	rs1593809
Chromosome Location	chr12:104071523-104071524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10861073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861074	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111710	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614418	0.81[EUR][1000 genomes]
rs12314920	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12368532	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1863878	0.80[GIH][hapmap];0.86[MEX][hapmap]
rs4981017	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4981018	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4981031	0.87[ASW][hapmap];0.82[CHB][hapmap];0.81[TSI][hapmap]
rs58605677	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs697202	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7136870	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs7303939	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs7304095	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv865	chr12:104030102-104074864	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv560038	chr12:104053420-104092996	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1593809	EID3	cis	parietal	SCAN
rs1593809	GNN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104064000-104072000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr12:104065800-104075200	Enhancers	Fetal Intestine Large	intestine
3	chr12:104066800-104074600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr12:104068000-104073800	Weak transcription	Spleen	Spleen
5	chr12:104068400-104073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:104070200-104072400	Enhancers	Fetal Intestine Small	intestine
7	chr12:104070400-104071600	Enhancers	Colonic Mucosa	Colon
8	chr12:104070600-104072200	Enhancers	Duodenum Mucosa	Duodenum
9	chr12:104070800-104073600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:104071000-104071600	Enhancers	Brain Germinal Matrix	brain
11	chr12:104071000-104072000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:104071200-104071600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:104071200-104071600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:104071200-104071600	Enhancers	Pancreas	Pancrea
15	chr12:104071400-104071600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:104071400-104072200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:104071400-104074000	Weak transcription	Fetal Muscle Leg	muscle

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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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