Variant report

Variant	rs4680295
Chromosome Location	chr3:156358487-156358488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1397190	0.83[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs1397192	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16826679	0.87[EUR][1000 genomes]
rs4680294	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66808167	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67423646	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73168612	0.89[EUR][1000 genomes]
rs73168615	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680295	SSR3	cis	parietal	SCAN
rs4680295	MLF1	cis	cerebellum	SCAN
rs4680295	IQCJ	cis	parietal	SCAN
rs4680295	OTOL1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156348800-156360600	Weak transcription	Right Atrium	heart
2	chr3:156349400-156361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:156351800-156361000	Weak transcription	Fetal Stomach	stomach
4	chr3:156353200-156358800	Weak transcription	GM12878-XiMat	blood
5	chr3:156354400-156359000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:156355800-156360200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:156355800-156367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:156356200-156361200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:156356200-156361600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:156357400-156360600	Weak transcription	K562	blood
11	chr3:156358400-156358800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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