Variant report

Variant	rs12118116
Chromosome Location	chr1:95774330-95774331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10874912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874914	0.85[AMR][1000 genomes]
rs11165366	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165367	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165374	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11165375	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11165379	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116466	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135605	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141215	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142805	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12752448	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548278	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17589093	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2182021	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34009737	0.80[AMR][1000 genomes]
rs34988332	0.84[AMR][1000 genomes]
rs4129611	0.84[AMR][1000 genomes]
rs4359066	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394708	0.82[EUR][1000 genomes]
rs4408199	0.81[AMR][1000 genomes]
rs4604740	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61771812	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66930640	0.84[AMR][1000 genomes]
rs72723875	0.87[AMR][1000 genomes]
rs912648	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927703	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	nsv830648	chr1:95760162-95926264	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1006113	chr1:95768502-96139003	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12118116	OR8B4	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95768400-95775000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:95769200-95782000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:95772800-95777400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:95773600-95774600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:95773800-95774400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:95773800-95774400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:95773800-95774400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:95773800-95774600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:95773800-95774600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:95773800-95774600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:95773800-95774600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:95773800-95774600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:95773800-95775400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:95773800-95775600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:95773800-95775600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:95773800-95778200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:95774000-95774400	Enhancers	Fetal Lung	lung
18	chr1:95774000-95774600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:95774000-95774600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:95774000-95774800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:95774000-95774800	Enhancers	Fetal Stomach	stomach
22	chr1:95774000-95775800	Enhancers	Brain Germinal Matrix	brain
23	chr1:95774200-95774600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:95774200-95774600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:95774200-95774600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:95774200-95774600	Enhancers	Brain Substantia Nigra	brain
27	chr1:95774200-95775000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:95774200-95775200	Enhancers	HUES48 Cell Line	embryonic stem cell

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