Variant report

Variant	rs1009873
Chromosome Location	chr3:157185611-157185612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11709669	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12631456	0.82[CHD][hapmap]
rs1378800	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1456100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1456101	0.96[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456102	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17391399	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1838143	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679795	0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4679798	0.82[CHD][hapmap]
rs6794511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	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
3	nsv963283	chr3:157183446-157186979	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1009873	C3orf55	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr3:157161200-157186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:157170200-157187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:157180200-157186000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:157180800-157186000	Enhancers	NHDF-Ad	bronchial
6	chr3:157181000-157186400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:157182800-157190400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:157183000-157188400	Weak transcription	Fetal Stomach	stomach
9	chr3:157184200-157187000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:157184400-157190400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:157184600-157185800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:157184600-157186000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:157184600-157186000	Genic enhancers	Osteobl	bone
14	chr3:157184600-157186200	Genic enhancers	HUVEC	blood vessel
15	chr3:157184800-157186000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:157184800-157186000	Enhancers	NHLF	lung
17	chr3:157185400-157185800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:157185400-157187200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:157185600-157185800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:157185600-157186600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:157185600-157186800	Weak transcription	NH-A	brain
22	chr3:157185600-157187000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:157185600-157187200	Weak transcription	Adipose Nuclei	Adipose
24	chr3:157185600-157189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:157185600-157211400	Weak transcription	HSMM	muscle

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