Variant report

Variant	rs3731489
Chromosome Location	chr3:48228906-48228907
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48226160..48232247-chr3:48279704..48285684,8	K562	blood:
2	chr12:121018252..121018999-chr3:48228737..48229264,2	Hela-S3	cervix:
3	chr3:48228556..48231473-chr3:48592024..48594297,2	K562	blood:
4	chr3:48227952..48231564-chr3:48487479..48489526,3	K562	blood:
5	chr3:48213772..48215466-chr3:48227696..48229218,2	K562	blood:
6	chr3:48129161..48131606-chr3:48228200..48230674,2	MCF-7	breast:
7	chr3:48227952..48230127-chr3:48487566..48489526,2	K562	blood:
8	chr3:48218514..48223617-chr3:48225606..48230757,7	MCF-7	breast:
9	chr3:48200857..48202800-chr3:48228103..48229714,2	MCF-7	breast:
10	chr3:48228787..48232242-chr3:48236568..48239852,3	K562	blood:
11	chr3:48228367..48230257-chr3:48281144..48282657,2	MCF-7	breast:
12	chr3:48219782..48224814-chr3:48228245..48230574,5	MCF-7	breast:
13	chr3:48228234..48229903-chr3:48593105..48594708,2	K562	blood:
14	chr3:47866553..47869509-chr3:48227817..48230002,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164048	Chromatin interaction
ENSG00000231884	Chromatin interaction
ENSG00000265483	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000235627	Chromatin interaction
ENSG00000132153	Chromatin interaction
ENSG00000047849	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000253056	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs11130164	0.82[EUR][1000 genomes]
rs11706221	0.81[EUR][1000 genomes]
rs11706277	0.83[EUR][1000 genomes]
rs11707606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707997	0.81[EUR][1000 genomes]
rs11709691	0.86[EUR][1000 genomes]
rs11710257	0.81[EUR][1000 genomes]
rs11710861	0.86[EUR][1000 genomes]
rs11714176	0.83[EUR][1000 genomes]
rs11714944	0.81[EUR][1000 genomes]
rs11715799	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716371	0.81[EUR][1000 genomes]
rs11716848	0.81[EUR][1000 genomes]
rs11717716	0.81[EUR][1000 genomes]
rs11718329	0.86[EUR][1000 genomes]
rs11718350	0.83[EUR][1000 genomes]
rs11719365	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11928691	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059037	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13060020	0.81[EUR][1000 genomes]
rs13061269	0.81[EUR][1000 genomes]
rs13066044	0.81[EUR][1000 genomes]
rs13066758	0.84[EUR][1000 genomes]
rs13067450	0.84[EUR][1000 genomes]
rs13068265	0.86[EUR][1000 genomes]
rs13069029	0.83[EUR][1000 genomes]
rs13070210	0.83[EUR][1000 genomes]
rs13071960	0.82[EUR][1000 genomes]
rs13072018	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079728	0.84[EUR][1000 genomes]
rs13081169	0.83[EUR][1000 genomes]
rs13081633	0.83[EUR][1000 genomes]
rs13082158	0.81[EUR][1000 genomes]
rs13082859	0.84[EUR][1000 genomes]
rs13084616	0.84[EUR][1000 genomes]
rs13085251	0.84[EUR][1000 genomes]
rs13087929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090538	0.82[EUR][1000 genomes]
rs13094727	0.86[EUR][1000 genomes]
rs13095983	0.83[EUR][1000 genomes]
rs13097450	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13099560	0.85[EUR][1000 genomes]
rs13100815	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17647717	0.85[EUR][1000 genomes]
rs17786132	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2125482	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2361685	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541	0.84[EUR][1000 genomes]
rs3197223	0.84[EUR][1000 genomes]
rs34076262	0.82[EUR][1000 genomes]
rs34225441	0.83[EUR][1000 genomes]
rs34513961	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34523942	0.84[EUR][1000 genomes]
rs34589064	0.84[EUR][1000 genomes]
rs34630841	0.84[EUR][1000 genomes]
rs34728236	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34749846	0.84[EUR][1000 genomes]
rs34946886	0.84[EUR][1000 genomes]
rs35190747	0.84[EUR][1000 genomes]
rs35297395	0.84[EUR][1000 genomes]
rs35411187	0.83[EUR][1000 genomes]
rs35414021	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35456569	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35778847	0.84[EUR][1000 genomes]
rs35802497	0.84[EUR][1000 genomes]
rs35942721	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35944878	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36020562	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36064160	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36075665	0.84[EUR][1000 genomes]
rs36092070	0.86[EUR][1000 genomes]
rs36121690	0.84[EUR][1000 genomes]
rs3729577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731497	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731534	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731550	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3937	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130522	0.83[EUR][1000 genomes]
rs4131361	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131362	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4371540	0.83[EUR][1000 genomes]
rs4392440	0.84[EUR][1000 genomes]
rs4420898	0.81[EUR][1000 genomes]
rs4479622	0.84[EUR][1000 genomes]
rs4511915	0.84[EUR][1000 genomes]
rs4511916	0.84[EUR][1000 genomes]
rs4541431	0.82[EUR][1000 genomes]
rs4619808	0.82[EUR][1000 genomes]
rs4632568	0.82[EUR][1000 genomes]
rs6442111	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775179	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782166	0.83[EUR][1000 genomes]
rs6791930	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793150	0.83[EUR][1000 genomes]
rs6793223	0.82[EUR][1000 genomes]
rs6793239	0.83[EUR][1000 genomes]
rs6794644	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796343	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796490	0.85[EUR][1000 genomes]
rs6800492	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6801801	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804986	0.82[EUR][1000 genomes]
rs71323391	0.84[EUR][1000 genomes]
rs71323394	0.83[EUR][1000 genomes]
rs71323395	0.81[EUR][1000 genomes]
rs71323396	0.81[EUR][1000 genomes]
rs71323397	0.81[EUR][1000 genomes]
rs745116	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7614532	0.83[EUR][1000 genomes]
rs7621785	0.84[EUR][1000 genomes]
rs7624450	0.84[EUR][1000 genomes]
rs7632297	0.83[EUR][1000 genomes]
rs7636461	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645425	0.82[EUR][1000 genomes]
rs7647817	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648720	0.85[EUR][1000 genomes]
rs7652233	0.82[EUR][1000 genomes]
rs7653152	0.81[EUR][1000 genomes]
rs7653336	0.82[EUR][1000 genomes]
rs9311421	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs936426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936427	0.86[EUR][1000 genomes]
rs9818937	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9819094	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9825637	0.82[EUR][1000 genomes]
rs9830016	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9831531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833309	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9834095	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837228	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847953	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850672	0.86[EUR][1000 genomes]
rs9853804	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862131	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	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
9	esv3408723	chr3:48228173-48230921	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs3731489	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs3731489	MRPS18AP1	cis	lung	GTEx
rs3731489	ZNF589	cis	Artery Tibial	GTEx
rs3731489	MRPS18AP1	cis	Nerve Tibial	GTEx
rs3731489	ZNF589	cis	Adipose Subcutaneous	GTEx
rs3731489	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3731489	ZNF589	cis	Nerve Tibial	GTEx
rs3731489	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs3731489	CDC25A	cis	Artery Tibial	GTEx
rs3731489	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs3731489	MRPS18AP1	cis	Artery Aorta	GTEx
rs3731489	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs3731489	ZNF589	cis	Esophagus Mucosa	GTEx
rs3731489	FCF1P2	cis	Artery Tibial	GTEx
rs3731489	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs3731489	NME6	cis	multi-tissue	Pritchard
rs3731489	NME6	cis	Muscle Skeletal	GTEx
rs3731489	NME6	cis	Esophagus Muscularis	GTEx
rs3731489	ZNF589	cis	lung	GTEx
rs3731489	SPINK8	cis	Whole Blood	GTEx
rs3731489	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs3731489	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs3731489	ZNF589	cis	Thyroid	GTEx
rs3731489	MRPS18AP1	cis	Thyroid	GTEx
rs3731489	MRPS18AP1	cis	Artery Tibial	GTEx
rs3731489	CDC25A	cis	Muscle Skeletal	GTEx
rs3731489	ZNF589	cis	Esophagus Muscularis	GTEx
rs3731489	ZNF589	cis	Stomach	GTEx
rs3731489	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs3731489	CDC25A	cis	Adipose Subcutaneous	GTEx
rs3731489	NME6	cis	Nerve Tibial	GTEx
rs3731489	ZNF589	cis	Artery Aorta	GTEx
rs3731489	MRPS18AP1	cis	Stomach	GTEx
rs3731489	NME6	cis	Artery Tibial	GTEx
rs3731489	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs3731489	CDC25A	cis	Thyroid	GTEx
rs3731489	NME6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48223800-48229000	Weak transcription	Aorta	Aorta
2	chr3:48225600-48229000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:48228000-48229000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:48228000-48229000	Flanking Active TSS	HUVEC	blood vessel
5	chr3:48228000-48229400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:48228000-48230200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:48228000-48230200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:48228000-48230600	Active TSS	A549	lung
9	chr3:48228200-48229000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:48228200-48229000	Flanking Active TSS	Fetal Lung	lung
11	chr3:48228200-48229000	Flanking Active TSS	Osteobl	bone
12	chr3:48228200-48229200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:48228200-48229200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:48228200-48229200	Flanking Active TSS	NH-A	brain
15	chr3:48228200-48229400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:48228200-48229400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr3:48228200-48229400	Flanking Active TSS	Fetal Thymus	thymus
18	chr3:48228200-48229600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:48228200-48230200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:48228200-48230200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:48228200-48230400	Active TSS	NHDF-Ad	bronchial
22	chr3:48228400-48229000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr3:48228400-48229000	Enhancers	Liver	Liver
24	chr3:48228400-48229000	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr3:48228400-48229000	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:48228400-48229000	Flanking Active TSS	Fetal Stomach	stomach
27	chr3:48228400-48229000	Enhancers	Psoas Muscle	Psoas
28	chr3:48228400-48229000	Flanking Active TSS	Stomach Mucosa	stomach
29	chr3:48228400-48229200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:48228400-48229200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr3:48228400-48229200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:48228400-48229200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:48228400-48229200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr3:48228400-48229200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:48228400-48229400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:48228400-48229400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr3:48228400-48229400	Flanking Active TSS	Thymus	Thymus
38	chr3:48228400-48229400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr3:48228400-48229800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr3:48228400-48230000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:48228400-48230000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:48228400-48230200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr3:48228400-48230200	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:48228400-48230200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr3:48228400-48230400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:48228400-48230400	Active TSS	Gastric	stomach
47	chr3:48228400-48230600	Active TSS	Rectal Smooth Muscle	rectum
48	chr3:48228600-48229000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:48228600-48229000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr3:48228600-48229000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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