Variant report

Variant	rs3731497
Chromosome Location	chr3:48226553-48226554
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48226160..48232247-chr3:48279704..48285684,8	K562	blood:
2	chr3:48218514..48223617-chr3:48225606..48230757,7	MCF-7	breast:
3	chr3:48221961..48224816-chr3:48225047..48228042,2	MCF-7	breast:
4	chr3:48218046..48220290-chr3:48225246..48226755,2	K562	blood:
5	chr3:47422216..47424027-chr3:48225306..48227849,2	K562	blood:

Variant related genes	Relation type
ENSG00000231884	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000253056	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 146 )
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	0.86[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	0.90[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	0.90[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731489	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	0.86[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	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:8 , 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

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs3731497	NME6	cis	Esophagus Muscularis	GTEx
rs3731497	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs3731497	SPINK8	cis	Whole Blood	GTEx
rs3731497	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs3731497	ZNF589	cis	Artery Tibial	GTEx
rs3731497	MRPS18AP1	cis	Artery Tibial	GTEx
rs3731497	ZNF589	cis	lung	GTEx
rs3731497	ZNF589	cis	Stomach	GTEx
rs3731497	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs3731497	CDC25A	cis	Thyroid	GTEx
rs3731497	NME6	cis	Nerve Tibial	GTEx
rs3731497	ZNF589	cis	Esophagus Muscularis	GTEx
rs3731497	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs3731497	MRPS18AP1	cis	Nerve Tibial	GTEx
rs3731497	ZNF589	cis	Esophagus Mucosa	GTEx
rs3731497	MRPS18AP1	cis	Thyroid	GTEx
rs3731497	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs3731497	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs3731497	ZNF589	cis	Nerve Tibial	GTEx
rs3731497	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs3731497	CDC25A	cis	Adipose Subcutaneous	GTEx
rs3731497	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs3731497	ZNF589	cis	Thyroid	GTEx
rs3731497	ZNF589	cis	Artery Aorta	GTEx
rs3731497	MRPS18AP1	cis	Artery Aorta	GTEx
rs3731497	NME6	cis	multi-tissue	Pritchard
rs3731497	FCF1P2	cis	Artery Tibial	GTEx
rs3731497	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3731497	NME6	cis	Muscle Skeletal	GTEx
rs3731497	NME6	cis	Artery Tibial	GTEx
rs3731497	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs3731497	MRPS18AP1	cis	lung	GTEx
rs3731497	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs3731497	MRPS18AP1	cis	Stomach	GTEx
rs3731497	ZNF589	cis	Adipose Subcutaneous	GTEx
rs3731497	CDC25A	cis	Muscle Skeletal	GTEx
rs3731497	CDC25A	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48193000-48228400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:48193600-48228200	Weak transcription	Pancreas	Pancrea
3	chr3:48193800-48228400	Weak transcription	Adipose Nuclei	Adipose
4	chr3:48193800-48228600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:48193800-48228800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:48194000-48228400	Weak transcription	Right Ventricle	heart
7	chr3:48194000-48228800	Weak transcription	Left Ventricle	heart
8	chr3:48197600-48227200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:48197800-48227600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:48198400-48227600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:48198400-48227800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr3:48198400-48228000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:48198400-48228000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:48198400-48228200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:48198400-48228200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:48199000-48227600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:48199200-48227800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:48199600-48227000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:48199800-48228000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:48200000-48227600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:48200200-48227800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:48200400-48226600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:48203400-48228200	Weak transcription	Colonic Mucosa	Colon
24	chr3:48204400-48228400	Weak transcription	Fetal Brain Male	brain
25	chr3:48205000-48227600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:48205200-48228400	Weak transcription	Primary B cells from cord blood	blood
27	chr3:48205400-48227200	Strong transcription	HMEC	breast
28	chr3:48205400-48227600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:48206000-48228400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:48206000-48228400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:48206200-48228600	Weak transcription	Brain Anterior Caudate	brain
32	chr3:48207200-48228400	Weak transcription	Placenta	Placenta
33	chr3:48207200-48228400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:48207400-48228600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:48208400-48227000	Weak transcription	Gastric	stomach
36	chr3:48208400-48228200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:48209400-48228600	Weak transcription	Primary T cells from cord blood	blood
38	chr3:48212200-48227200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:48212200-48227400	Weak transcription	Stomach Mucosa	stomach
40	chr3:48212200-48227800	Strong transcription	Fetal Thymus	thymus
41	chr3:48212400-48226600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:48213400-48227400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:48213600-48227600	Strong transcription	A549	lung
44	chr3:48213600-48227800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:48213800-48227000	Strong transcription	HUVEC	blood vessel
46	chr3:48213800-48227200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:48213800-48227200	Strong transcription	Osteobl	bone
48	chr3:48214000-48227000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:48214200-48228400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:48214400-48228400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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