Variant report

Variant	rs1045482
Chromosome Location	chr3:48312229-48312230
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48309419..48312351-chr3:48467135..48471240,5	MCF-7	breast:
2	chr3:48308597..48312699-chr3:48540055..48542560,3	MCF-7	breast:
3	chr3:48309044..48314082-chr3:48470031..48473637,5	MCF-7	breast:
4	chr3:48228135..48231102-chr3:48309696..48312557,4	MCF-7	breast:
5	chr3:48229316..48231788-chr3:48310820..48313166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164050	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164045	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 50 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs11130162	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130163	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130164	0.81[EUR][1000 genomes]
rs1134867	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706221	0.80[EUR][1000 genomes]
rs11706277	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11707997	0.80[EUR][1000 genomes]
rs11709691	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11710257	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11710861	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11713476	0.89[EUR][1000 genomes]
rs11714176	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715799	0.81[EUR][1000 genomes]
rs11716371	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs11716848	0.80[EUR][1000 genomes]
rs11717716	0.80[EUR][1000 genomes]
rs11718329	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11718350	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11719365	0.83[EUR][1000 genomes]
rs11928691	0.85[EUR][1000 genomes]
rs13059037	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13060020	0.80[EUR][1000 genomes]
rs13061269	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs13066044	0.80[EUR][1000 genomes]
rs13066758	0.83[EUR][1000 genomes]
rs13067450	0.83[EUR][1000 genomes]
rs13068265	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs13069029	0.82[EUR][1000 genomes]
rs13070210	0.82[EUR][1000 genomes]
rs13071960	0.81[EUR][1000 genomes]
rs13072018	0.85[EUR][1000 genomes]
rs13079728	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13081169	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13081633	0.82[EUR][1000 genomes]
rs13082859	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13084616	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13085251	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13090538	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13094727	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13095983	0.82[EUR][1000 genomes]
rs13097450	0.84[EUR][1000 genomes]
rs13099560	1.00[YRI][hapmap]
rs13100815	0.83[EUR][1000 genomes]
rs17647717	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2125482	0.85[EUR][1000 genomes]
rs2541	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs3197223	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs34076262	0.81[EUR][1000 genomes]
rs34225441	0.83[EUR][1000 genomes]
rs34523942	0.83[EUR][1000 genomes]
rs34589064	0.83[EUR][1000 genomes]
rs34630841	0.83[EUR][1000 genomes]
rs34728236	0.83[EUR][1000 genomes]
rs34749846	0.83[EUR][1000 genomes]
rs34946886	0.83[EUR][1000 genomes]
rs35190747	0.83[EUR][1000 genomes]
rs35297395	0.83[EUR][1000 genomes]
rs35411187	0.82[EUR][1000 genomes]
rs35414021	0.83[EUR][1000 genomes]
rs35778847	0.83[EUR][1000 genomes]
rs35802497	0.83[EUR][1000 genomes]
rs35944878	0.84[EUR][1000 genomes]
rs36020562	0.82[EUR][1000 genomes]
rs36075665	0.83[EUR][1000 genomes]
rs36092070	0.86[EUR][1000 genomes]
rs36121690	0.83[EUR][1000 genomes]
rs3729577	0.87[CEU][hapmap]
rs3731513	0.87[CEU][hapmap]
rs3731555	0.88[CEU][hapmap]
rs3937	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4130522	0.82[EUR][1000 genomes]
rs4130995	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4131361	0.85[EUR][1000 genomes]
rs4131362	0.85[EUR][1000 genomes]
rs4371540	0.82[EUR][1000 genomes]
rs4392440	0.83[EUR][1000 genomes]
rs4420898	0.80[EUR][1000 genomes]
rs4479622	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4511915	0.83[EUR][1000 genomes]
rs4511916	0.83[EUR][1000 genomes]
rs4541431	0.81[EUR][1000 genomes]
rs4619808	0.81[EUR][1000 genomes]
rs4632568	0.81[EUR][1000 genomes]
rs6442110	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442111	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6775179	0.86[EUR][1000 genomes]
rs6782166	0.82[EUR][1000 genomes]
rs6787500	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791930	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6793150	0.82[EUR][1000 genomes]
rs6793223	0.81[EUR][1000 genomes]
rs6793239	0.82[EUR][1000 genomes]
rs6794644	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6796343	0.84[EUR][1000 genomes]
rs6796490	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6797587	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6800492	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6801801	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6804986	0.81[EUR][1000 genomes]
rs6806112	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]
rs71323391	0.84[EUR][1000 genomes]
rs71323394	0.82[EUR][1000 genomes]
rs71323395	0.80[EUR][1000 genomes]
rs71323397	0.80[EUR][1000 genomes]
rs7374376	0.96[YRI][hapmap]
rs745116	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7614532	0.83[EUR][1000 genomes]
rs7617773	0.84[CHD][hapmap]
rs7619865	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7621785	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7624450	0.83[EUR][1000 genomes]
rs7632297	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7636461	0.84[EUR][1000 genomes]
rs7644414	0.81[EUR][1000 genomes]
rs7645425	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7648720	0.85[EUR][1000 genomes]
rs7652233	0.83[EUR][1000 genomes]
rs7653152	0.82[EUR][1000 genomes]
rs7653336	0.81[EUR][1000 genomes]
rs9311421	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs936426	0.87[CEU][hapmap]
rs936427	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9818937	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9819094	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9825637	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9830016	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9833309	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9834095	0.85[EUR][1000 genomes]
rs9837228	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9846818	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847953	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9850672	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9853804	0.85[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:50)

SNP	Gene	Cis/trans	Tissue	Source
rs1045482	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs1045482	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs1045482	UQCRC1	cis	parietal	SCAN
rs1045482	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs1045482	ZNF589	cis	Temporal Cortex	GTEx
rs1045482	CDC25A	cis	Thyroid	GTEx
rs1045482	ARIH2	cis	parietal	SCAN
rs1045482	NME6	cis	Artery Tibial	GTEx
rs1045482	CDC25A	cis	cerebellum	SCAN
rs1045482	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs1045482	ZNF589	cis	parietal	SCAN
rs1045482	CDC25A	cis	Adipose Subcutaneous	GTEx
rs1045482	ALS2CL	cis	parietal	SCAN
rs1045482	ZNF589	cis	Thyroid	GTEx
rs1045482	MRPS18AP1	cis	Thyroid	GTEx
rs1045482	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs1045482	CDC25A	cis	Muscle Skeletal	GTEx
rs1045482	MRPS18AP1	cis	Nerve Tibial	GTEx
rs1045482	NME6	cis	cerebellum	SCAN
rs1045482	NME6	cis	Nerve Tibial	GTEx
rs1045482	ZNF589	cis	Brain Pons	GTEx
rs1045482	ZNF589	cis	cerebellum	SCAN
rs1045482	ZNF589	cis	Cerebellum	GTEx
rs1045482	MRPS18AP1	cis	Artery Aorta	GTEx
rs1045482	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs1045482	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1045482	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs1045482	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs1045482	NME6	cis	Artery Aorta	GTEx
rs1045482	MRPS18AP1	cis	Stomach	GTEx
rs1045482	ZNF589	cis	Esophagus Mucosa	GTEx
rs1045482	ZNF589	cis	lung	GTEx
rs1045482	ZNF589	cis	Nerve Tibial	GTEx
rs1045482	NME6	cis	multi-tissue	Pritchard
rs1045482	RBM5	cis	cerebellum	SCAN
rs1045482	MRPS18AP1	cis	lung	GTEx
rs1045482	ZNF589	cis	multi-tissue	Pritchard
rs1045482	ZNF589	cis	Artery Aorta	GTEx
rs1045482	ZNF589	cis	Frontal Cortex	GTEx
rs1045482	MRPS18AP1	cis	Artery Tibial	GTEx
rs1045482	ZNF589	cis	Stomach	GTEx
rs1045482	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1045482	ZNF589	cis	Adipose Subcutaneous	GTEx
rs1045482	NME6	cis	Esophagus Muscularis	GTEx
rs1045482	CDC25A	cis	Artery Tibial	GTEx
rs1045482	ZNF589	cis	Whole Blood	GTEx
rs1045482	FCF1P2	cis	Artery Tibial	GTEx
rs1045482	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs1045482	MRPS18AP1	cis	Whole Blood	GTEx
rs1045482	ZNF589	cis	Artery Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283400-48315200	Weak transcription	Ovary	ovary
2	chr3:48285600-48312400	Weak transcription	Psoas Muscle	Psoas
3	chr3:48288600-48312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:48289200-48312600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:48297800-48312400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:48299600-48312600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:48302800-48312800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:48303000-48317400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:48304800-48314000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:48305600-48318000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:48307000-48312400	Strong transcription	GM12878-XiMat	blood
12	chr3:48307000-48313000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:48307400-48313600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:48307600-48312600	Strong transcription	Brain Hippocampus Middle	brain
15	chr3:48307600-48312800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr3:48307600-48312800	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:48307600-48313000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:48307600-48314000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:48307800-48313400	Strong transcription	Fetal Brain Female	brain
20	chr3:48308800-48316800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:48309200-48313800	Strong transcription	Brain Germinal Matrix	brain
22	chr3:48309400-48312400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:48309400-48321000	Weak transcription	Right Atrium	heart
24	chr3:48309600-48312400	Strong transcription	Fetal Stomach	stomach
25	chr3:48309600-48317800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:48309800-48312400	Strong transcription	Brain Angular Gyrus	brain
27	chr3:48309800-48314000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:48310000-48312600	Strong transcription	Spleen	Spleen
29	chr3:48310000-48314600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:48310200-48313800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:48310200-48316000	Weak transcription	Hela-S3	cervix
32	chr3:48310400-48313000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:48310400-48314400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr3:48310600-48312400	Weak transcription	Left Ventricle	heart
35	chr3:48310600-48312800	Weak transcription	NHDF-Ad	bronchial
36	chr3:48310600-48313800	Weak transcription	Pancreas	Pancrea
37	chr3:48310600-48315000	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:48310800-48316400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:48310800-48316800	Weak transcription	HSMMtube	muscle
40	chr3:48310800-48330200	Weak transcription	Fetal Lung	lung
41	chr3:48311000-48312800	Weak transcription	HepG2	liver
42	chr3:48311000-48313200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:48311000-48314000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:48311000-48314400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr3:48311000-48314400	Weak transcription	Stomach Mucosa	stomach
46	chr3:48311000-48314600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr3:48311000-48315800	Weak transcription	Right Ventricle	heart
48	chr3:48311000-48333800	Weak transcription	Brain Anterior Caudate	brain
49	chr3:48311200-48312800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:48311200-48313000	Weak transcription	HUVEC	blood vessel

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