Variant report

Variant	rs4679798
Chromosome Location	chr3:157187570-157187571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1009873	0.82[CHD][hapmap]
rs12631456	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378794	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17470517	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1824056	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1902347	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28690487	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680370	0.94[CEU][hapmap]
rs57095742	0.88[EUR][1000 genomes]
rs6794511	0.89[CHB][hapmap]
rs7639175	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9815250	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9841781	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9851066	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9859018	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9873474	0.94[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9877620	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4679798	C3orf55	cis	cerebellum	SCAN
rs4679798	KPNA4	cis	parietal	SCAN
rs4679798	B3GALNT1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157160400-157195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:157182800-157190400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:157183000-157188400	Weak transcription	Fetal Stomach	stomach
4	chr3:157184400-157190400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:157185600-157189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:157185600-157211400	Weak transcription	HSMM	muscle
7	chr3:157186000-157188000	Strong transcription	Osteobl	bone
8	chr3:157186000-157193400	Weak transcription	NHLF	lung
9	chr3:157186600-157187600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:157186600-157188200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:157186800-157187800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:157187000-157187600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:157187000-157187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:157187000-157187800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:157187000-157188000	Strong transcription	HUVEC	blood vessel
16	chr3:157187000-157188200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:157187000-157188200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:157187000-157189400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:157187200-157187800	Enhancers	Adipose Nuclei	Adipose
20	chr3:157187200-157188000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:157187200-157189800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:157187400-157193600	Weak transcription	NH-A	brain

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