Variant report

Variant	rs6806112
Chromosome Location	chr3:48276077-48276078
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48227576..48230512-chr3:48272332..48276184,3	K562	blood:

Variant related genes	Relation type
ENSG00000164045	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 48 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1045482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130162	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130163	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1134867	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706277	0.84[CEU][hapmap]
rs11709691	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11710257	0.84[CEU][hapmap]
rs11710861	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11713476	0.86[EUR][1000 genomes]
rs11714176	0.84[CEU][hapmap]
rs11715799	0.84[EUR][1000 genomes]
rs11716371	0.84[CEU][hapmap]
rs11718329	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11718350	0.84[CEU][hapmap]
rs11719365	0.85[EUR][1000 genomes]
rs11928691	0.85[EUR][1000 genomes]
rs13059037	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13061269	0.81[CEU][hapmap]
rs13066758	0.81[EUR][1000 genomes]
rs13067450	0.81[EUR][1000 genomes]
rs13068265	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072018	0.83[EUR][1000 genomes]
rs13079728	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs13081169	0.81[CEU][hapmap]
rs13082859	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs13084616	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13085251	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13090538	0.84[CEU][hapmap]
rs13094727	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs13097450	0.86[EUR][1000 genomes]
rs13099560	1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13100815	0.83[EUR][1000 genomes]
rs17647717	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17786132	0.80[EUR][1000 genomes]
rs2125482	0.83[EUR][1000 genomes]
rs2541	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3197223	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs34225441	0.81[EUR][1000 genomes]
rs34523942	0.81[EUR][1000 genomes]
rs34589064	0.81[EUR][1000 genomes]
rs34630841	0.81[EUR][1000 genomes]
rs34728236	0.85[EUR][1000 genomes]
rs34749846	0.81[EUR][1000 genomes]
rs34946886	0.81[EUR][1000 genomes]
rs35190747	0.81[EUR][1000 genomes]
rs35297395	0.81[EUR][1000 genomes]
rs35414021	0.81[EUR][1000 genomes]
rs35456569	0.80[EUR][1000 genomes]
rs35778847	0.81[EUR][1000 genomes]
rs35802497	0.81[EUR][1000 genomes]
rs35944878	0.82[EUR][1000 genomes]
rs36020562	0.84[EUR][1000 genomes]
rs36075665	0.81[EUR][1000 genomes]
rs36092070	0.84[EUR][1000 genomes]
rs36121690	0.81[EUR][1000 genomes]
rs3729577	0.84[CEU][hapmap]
rs3731513	0.84[CEU][hapmap]
rs3731555	0.85[CEU][hapmap]
rs3937	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4130995	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4131361	0.83[EUR][1000 genomes]
rs4131362	0.83[EUR][1000 genomes]
rs4392440	0.81[EUR][1000 genomes]
rs4479622	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4511915	0.81[EUR][1000 genomes]
rs4511916	0.80[EUR][1000 genomes]
rs6442108	0.81[CEU][hapmap]
rs6442110	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442111	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6766754	0.81[CEU][hapmap]
rs6775179	0.84[EUR][1000 genomes]
rs6787500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791930	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6794644	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6796343	0.84[EUR][1000 genomes]
rs6796490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6797587	0.81[CHB][hapmap]
rs6800492	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6801801	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs71323391	0.82[EUR][1000 genomes]
rs7374376	0.80[CEU][hapmap];0.97[YRI][hapmap]
rs745116	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7614532	0.80[EUR][1000 genomes]
rs7619865	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7621785	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7624450	0.80[EUR][1000 genomes]
rs7632297	0.82[EUR][1000 genomes]
rs7636461	0.86[EUR][1000 genomes]
rs7645425	0.81[CEU][hapmap]
rs7648720	0.83[EUR][1000 genomes]
rs7652233	0.81[EUR][1000 genomes]
rs9311421	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs936426	0.87[CEU][hapmap]
rs936427	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9818937	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs9819094	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs9825637	0.84[CEU][hapmap]
rs9830016	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9833309	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9834095	0.83[EUR][1000 genomes]
rs9837228	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs9846818	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9847953	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs9850672	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs9853804	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:48)

SNP	Gene	Cis/trans	Tissue	Source
rs6806112	NME6	cis	Artery Tibial	GTEx
rs6806112	FCF1P2	cis	Artery Tibial	GTEx
rs6806112	ZNF589	cis	multi-tissue	Pritchard
rs6806112	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6806112	ZNF589	cis	Temporal Cortex	GTEx
rs6806112	ZNF589	cis	intralobular white matter	BrainEAC
rs6806112	NME6	cis	multi-tissue	Pritchard
rs6806112	MRPS18AP1	cis	Artery Tibial	GTEx
rs6806112	ZNF589	cis	Stomach	GTEx
rs6806112	MRPS18AP1	cis	Whole Blood	GTEx
rs6806112	ZNF589	cis	Brain Pons	GTEx
rs6806112	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6806112	ZNF589	cis	hippocampus	BrainEAC
rs6806112	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs6806112	NME6	cis	Esophagus Muscularis	GTEx
rs6806112	ZNF589	cis	Frontal Cortex	GTEx
rs6806112	ZNF589	cis	Whole Blood	GTEx
rs6806112	ZNF589	cis	Nerve Tibial	GTEx
rs6806112	NME6	cis	Nerve Tibial	GTEx
rs6806112	ZNF589	cis	brain	BrainEAC
rs6806112	MRPS18AP1	cis	Thyroid	GTEx
rs6806112	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6806112	ZNF589	cis	occipital cortex	BrainEAC
rs6806112	ZNF589	cis	lung	GTEx
rs6806112	ZNF589	cis	Artery Aorta	GTEx
rs6806112	ZNF589	cis	Thyroid	GTEx
rs6806112	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6806112	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6806112	MRPS18AP1	cis	Artery Aorta	GTEx
rs6806112	MRPS18AP1	cis	Stomach	GTEx
rs6806112	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6806112	CDC25A	cis	Artery Tibial	GTEx
rs6806112	MRPS18AP1	cis	lung	GTEx
rs6806112	ZNF589	cis	Lymphoblastoid	GTEx
rs6806112	CDC25A	cis	Thyroid	GTEx
rs6806112	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs6806112	ZNF589	cis	Adipose Subcutaneous	GTEx
rs6806112	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs6806112	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6806112	CDC25A	cis	Muscle Skeletal	GTEx
rs6806112	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs6806112	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6806112	ZNF589	cis	cerebellar cortex	BrainEAC
rs6806112	ZNF589	cis	Artery Tibial	GTEx
rs6806112	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs6806112	NME6	cis	Artery Aorta	GTEx
rs6806112	ZNF589	cis	Cerebellum	GTEx
rs6806112	ZNF589	cis	Esophagus Mucosa	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48265800-48277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:48274000-48276400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:48274000-48276600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:48274000-48277600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:48274000-48282400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:48274400-48277800	Weak transcription	Thymus	Thymus
7	chr3:48274600-48276800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:48274600-48277400	Weak transcription	Fetal Thymus	thymus
9	chr3:48274600-48277800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:48274600-48277800	Weak transcription	Esophagus	oesophagus
11	chr3:48274600-48277800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:48274600-48278000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:48274600-48278000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:48274600-48278000	Weak transcription	Spleen	Spleen
15	chr3:48274600-48278200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:48274600-48278400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:48274600-48281200	Weak transcription	Brain Germinal Matrix	brain
18	chr3:48274600-48281400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:48274600-48281800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:48274600-48282200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:48274600-48282200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:48274600-48282200	Weak transcription	Ovary	ovary
23	chr3:48274800-48277200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:48274800-48277400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:48274800-48278000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:48274800-48278000	Weak transcription	NHDF-Ad	bronchial
27	chr3:48274800-48278200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:48274800-48278200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:48274800-48281200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:48274800-48282000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:48274800-48282000	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:48274800-48282000	Weak transcription	HMEC	breast
33	chr3:48275000-48277200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:48275000-48282200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:48275200-48277400	Weak transcription	K562	blood
36	chr3:48275400-48276800	Weak transcription	HepG2	liver
37	chr3:48275400-48277800	Weak transcription	Primary B cells from cord blood	blood
38	chr3:48276000-48276200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:48276000-48276200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:48276000-48281800	Weak transcription	GM12878-XiMat	blood

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