Variant report

Variant	rs6775179
Chromosome Location	chr3:48313418-48313419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48312759..48319718-chr3:48469447..48473702,8	MCF-7	breast:
2	chr3:48313306..48315855-chr3:48341365..48343268,2	MCF-7	breast:
3	chr3:48309044..48314082-chr3:48470031..48473637,5	MCF-7	breast:
4	chr3:48235794..48238094-chr3:48312692..48314952,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172113	Chromatin interaction
ENSG00000265483	Chromatin interaction
ENSG00000164050	Chromatin interaction

Extended variants
information (count: 153 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1045482	0.86[EUR][1000 genomes]
rs11130162	0.86[EUR][1000 genomes]
rs11130163	0.86[EUR][1000 genomes]
rs11130164	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1134867	0.81[EUR][1000 genomes]
rs11706221	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706277	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707606	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707997	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11709691	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710257	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11710861	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713476	0.82[EUR][1000 genomes]
rs11714176	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714944	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715776	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715799	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11715876	0.86[EUR][1000 genomes]
rs11716371	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11716848	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717716	0.94[EUR][1000 genomes]
rs11718329	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11718350	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719365	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11928691	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13059037	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13060020	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061269	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066044	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066758	0.97[EUR][1000 genomes]
rs13067450	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13068265	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13068288	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13069029	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13070210	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13071960	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13072018	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079728	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13081169	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13081633	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13082158	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13082859	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13084616	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13085251	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087929	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090538	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13094727	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095983	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13097450	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13100815	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17647717	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17786132	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2125482	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361685	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2541	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3197223	0.97[EUR][1000 genomes]
rs34076262	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34225441	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34523942	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34589064	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34630841	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34728236	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34749846	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34946886	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35190747	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35297395	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35297486	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35411187	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35414021	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35456569	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35778847	0.97[EUR][1000 genomes]
rs35802497	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35944878	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36020562	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36064160	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36075665	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36092070	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36121690	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3729577	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731487	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731489	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731497	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731513	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731515	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731534	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731550	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731555	0.85[EUR][1000 genomes]
rs3937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130522	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130995	0.80[EUR][1000 genomes]
rs4131361	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4131362	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4371540	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4392440	0.97[EUR][1000 genomes]
rs4404473	0.91[EUR][1000 genomes]
rs4420898	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4479622	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4511915	0.97[EUR][1000 genomes]
rs4511916	0.96[EUR][1000 genomes]
rs4541431	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4619808	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4632568	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442110	0.86[EUR][1000 genomes]
rs6442111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782166	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6787500	0.86[EUR][1000 genomes]
rs6791930	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793150	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6793223	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6793239	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794644	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796343	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800492	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804986	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6806112	0.84[EUR][1000 genomes]
rs71323391	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71323394	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71323395	0.94[EUR][1000 genomes]
rs71323396	0.93[EUR][1000 genomes]
rs71323397	0.94[EUR][1000 genomes]
rs745116	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7614532	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7621785	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7624450	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632297	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7636461	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644414	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7645425	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647817	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7648720	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7652233	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7653152	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7653336	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9311421	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936426	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936427	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818937	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819094	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825637	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9830016	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9831531	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9833309	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834095	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847953	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850672	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853804	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862131	0.80[EUR][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	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
2	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
3	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
4	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs6775179	ZNF589	cis	Nerve Tibial	GTEx
rs6775179	NME6	cis	Esophagus Muscularis	GTEx
rs6775179	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6775179	ZNF589	cis	Esophagus Mucosa	GTEx
rs6775179	MRPS18AP1	cis	Stomach	GTEx
rs6775179	ZNF589	cis	Artery Tibial	GTEx
rs6775179	MRPS18AP1	cis	Artery Aorta	GTEx
rs6775179	NME6	cis	Artery Tibial	GTEx
rs6775179	MRPS18AP1	cis	lung	GTEx
rs6775179	ZNF589	cis	Stomach	GTEx
rs6775179	CDC25A	cis	Muscle Skeletal	GTEx
rs6775179	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6775179	MRPS18AP1	cis	Thyroid	GTEx
rs6775179	MRPS18AP1	cis	Artery Tibial	GTEx
rs6775179	NME6	cis	Muscle Skeletal	GTEx
rs6775179	CDC25A	cis	Artery Tibial	GTEx
rs6775179	ZNF589	cis	Artery Aorta	GTEx
rs6775179	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6775179	FCF1P2	cis	Artery Tibial	GTEx
rs6775179	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6775179	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6775179	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6775179	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6775179	ZNF589	cis	Thyroid	GTEx
rs6775179	ZNF589	cis	Esophagus Muscularis	GTEx
rs6775179	CDC25A	cis	Thyroid	GTEx
rs6775179	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs6775179	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6775179	NME6	cis	Nerve Tibial	GTEx
rs6775179	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs6775179	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs6775179	NME6	cis	multi-tissue	Pritchard
rs6775179	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs6775179	NME6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283400-48315200	Weak transcription	Ovary	ovary
2	chr3:48303000-48317400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:48304800-48314000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:48305600-48318000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:48307400-48313600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:48307600-48314000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:48308800-48316800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:48309200-48313800	Strong transcription	Brain Germinal Matrix	brain
9	chr3:48309400-48321000	Weak transcription	Right Atrium	heart
10	chr3:48309600-48317800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:48309800-48314000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:48310000-48314600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:48310200-48313800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:48310200-48316000	Weak transcription	Hela-S3	cervix
15	chr3:48310400-48314400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
16	chr3:48310600-48313800	Weak transcription	Pancreas	Pancrea
17	chr3:48310600-48315000	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:48310800-48316400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:48310800-48316800	Weak transcription	HSMMtube	muscle
20	chr3:48310800-48330200	Weak transcription	Fetal Lung	lung
21	chr3:48311000-48314000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:48311000-48314400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
23	chr3:48311000-48314400	Weak transcription	Stomach Mucosa	stomach
24	chr3:48311000-48314600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr3:48311000-48315800	Weak transcription	Right Ventricle	heart
26	chr3:48311000-48333800	Weak transcription	Brain Anterior Caudate	brain
27	chr3:48311200-48315600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:48311200-48317400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:48311200-48317800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:48311200-48318000	Weak transcription	Gastric	stomach
31	chr3:48311200-48330800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:48311200-48334400	Weak transcription	Aorta	Aorta
33	chr3:48311400-48314800	Weak transcription	Adipose Nuclei	Adipose
34	chr3:48311400-48315400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:48311400-48333400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:48311400-48334200	Weak transcription	Thymus	Thymus
37	chr3:48311600-48313800	Weak transcription	Esophagus	oesophagus
38	chr3:48311600-48314800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:48311600-48330800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:48311600-48334200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:48311600-48334200	Weak transcription	Liver	Liver
42	chr3:48311800-48313600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:48311800-48314200	Weak transcription	Fetal Brain Male	brain
44	chr3:48311800-48314800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:48311800-48315200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:48311800-48315400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:48311800-48316800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:48311800-48329800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:48312000-48313600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:48312000-48314400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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