Variant report

Variant	rs4939097
Chromosome Location	chr11:56652705-56652706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11228836	0.81[ASN][1000 genomes]
rs11603620	0.81[ASN][1000 genomes]
rs11828859	1.00[JPT][hapmap]
rs12416998	0.81[ASN][1000 genomes]
rs12419314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421316	1.00[JPT][hapmap]
rs1613887	0.97[ASN][1000 genomes]
rs1632332	0.95[ASN][1000 genomes]
rs17640838	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17640885	0.84[ASN][1000 genomes]
rs1783444	0.97[ASN][1000 genomes]
rs1783445	0.97[ASN][1000 genomes]
rs1783446	0.97[ASN][1000 genomes]
rs1783447	0.97[ASN][1000 genomes]
rs1783450	0.95[ASN][1000 genomes]
rs1783451	0.97[ASN][1000 genomes]
rs1783459	0.99[ASN][1000 genomes]
rs1783465	0.97[ASN][1000 genomes]
rs1792494	0.97[ASN][1000 genomes]
rs1792495	0.97[ASN][1000 genomes]
rs1792496	0.97[ASN][1000 genomes]
rs1792498	0.97[ASN][1000 genomes]
rs1792499	0.97[ASN][1000 genomes]
rs1792500	0.95[ASN][1000 genomes]
rs1892787	0.97[ASN][1000 genomes]
rs1938751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938753	0.81[ASN][1000 genomes]
rs1938759	0.84[ASN][1000 genomes]
rs1938760	0.84[ASN][1000 genomes]
rs2226850	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226851	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374	0.97[ASN][1000 genomes]
rs4939095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523098	0.97[ASN][1000 genomes]
rs56210588	1.00[ASN][1000 genomes]
rs68039795	0.80[ASN][1000 genomes]
rs7118645	0.84[ASN][1000 genomes]
rs7119402	0.81[ASN][1000 genomes]
rs731744	0.81[ASN][1000 genomes]
rs737368	0.84[ASN][1000 genomes]
rs7930832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940288	0.81[ASN][1000 genomes]
rs7943283	0.81[ASN][1000 genomes]
rs7947879	0.84[ASN][1000 genomes]
rs947805	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468577	chr11:56503728-56704042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555101	chr11:56503728-56704042	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv469960	chr11:56605222-56704042	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1045889	chr11:56624365-56737435	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4939097	OR8J1	cis	parietal	SCAN
rs4939097	OR5M11	cis	cerebellum	SCAN
rs4939097	OR5M10	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56651200-56654800	Enhancers	Fetal Intestine Large	intestine
2	chr11:56652000-56652800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:56652000-56653200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:56652000-56654800	Enhancers	Fetal Intestine Small	intestine
5	chr11:56652000-56654800	Enhancers	Stomach Mucosa	stomach
6	chr11:56652200-56653200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:56652200-56653400	Enhancers	Fetal Lung	lung
8	chr11:56652200-56654400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr11:56652200-56654600	Enhancers	Duodenum Mucosa	Duodenum
10	chr11:56652200-56654800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:56652200-56655000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:56652400-56652800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:56652400-56652800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:56652400-56653000	Enhancers	Pancreas	Pancrea
15	chr11:56652400-56653200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:56652600-56652800	Enhancers	Gastric	stomach
17	chr11:56652600-56652800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr11:56652600-56653000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:56652600-56653000	Flanking Active TSS	A549	lung
20	chr11:56652600-56653200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:56652600-56653200	Enhancers	NHEK	skin
22	chr11:56652600-56653800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr11:56652600-56654600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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