Variant report

Variant	rs7647817
Chromosome Location	chr3:48236507-48236508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:48235742-48236551	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr3:48235953-48236532	Hela-S3	cervix:	n/a	chr3:48236368-48236379
3	CTCF	chr3:48235697-48236550	A549	lung:	n/a	chr3:48236090-48236108 chr3:48236092-48236113 chr3:48236093-48236106
4	CTCF	chr3:48235701-48236515	SK-N-SH	brain:	n/a	chr3:48236090-48236108 chr3:48236092-48236113 chr3:48236093-48236106
5	CTCF	chr3:48236380-48236530	NHLF	lung:	n/a	n/a
6	RAD21	chr3:48235700-48236511	HCT-116	colon:	n/a	chr3:48236091-48236110
7	RAD21	chr3:48235834-48236547	HCT-116	colon:	n/a	chr3:48236091-48236110

No.	Distal block	Cell Line	Cell type
1	chr3:48235536..48236555-chr3:48476745..48477999,5	K562	blood:
2	chr3:48235629..48237322-chr3:48585256..48587869,2	K562	blood:
3	chr3:48235629..48237555-chr3:48585079..48587869,3	K562	blood:
4	chr3:48229925..48231959-chr3:48234100..48237054,2	K562	blood:

Variant related genes	Relation type
MIR4443	TF binding region
ENSG00000114268	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	0.93[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	0.86[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	0.86[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731489	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731497	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	0.93[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]
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
rs7647817	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs7647817	CDC25A	cis	Muscle Skeletal	GTEx
rs7647817	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs7647817	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7647817	MRPS18AP1	cis	Artery Aorta	GTEx
rs7647817	MRPS18AP1	cis	lung	GTEx
rs7647817	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs7647817	MRPS18AP1	cis	Thyroid	GTEx
rs7647817	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs7647817	ZNF589	cis	Artery Tibial	GTEx
rs7647817	ZNF589	cis	Stomach	GTEx
rs7647817	ZNF589	cis	Thyroid	GTEx
rs7647817	NME6	cis	multi-tissue	Pritchard
rs7647817	SPINK8	cis	Whole Blood	GTEx
rs7647817	ZNF589	cis	Esophagus Muscularis	GTEx
rs7647817	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs7647817	ZNF589	cis	Artery Aorta	GTEx
rs7647817	FCF1P2	cis	Artery Tibial	GTEx
rs7647817	ZNF589	cis	Nerve Tibial	GTEx
rs7647817	ZNF589	cis	Adipose Subcutaneous	GTEx
rs7647817	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7647817	MRPS18AP1	cis	Artery Tibial	GTEx
rs7647817	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs7647817	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs7647817	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7647817	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7647817	CDC25A	cis	Thyroid	GTEx
rs7647817	CDC25A	cis	Artery Tibial	GTEx
rs7647817	NME6	cis	Muscle Skeletal	GTEx
rs7647817	NME6	cis	Artery Tibial	GTEx
rs7647817	ZNF589	cis	Esophagus Mucosa	GTEx
rs7647817	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs7647817	CDC25A	cis	Adipose Subcutaneous	GTEx
rs7647817	ZNF589	cis	lung	GTEx
rs7647817	NME6	cis	Esophagus Muscularis	GTEx
rs7647817	NME6	cis	Nerve Tibial	GTEx
rs7647817	MRPS18AP1	cis	Stomach	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48230600-48237800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:48230600-48238400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:48230600-48238400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:48232600-48241800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:48232800-48237800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:48232800-48238000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:48232800-48238000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:48232800-48244200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:48233000-48238000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:48235600-48236600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:48235800-48236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:48235800-48236600	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:48235800-48236600	Enhancers	Dnd41	blood
14	chr3:48235800-48236600	Enhancers	GM12878-XiMat	blood
15	chr3:48235800-48237800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:48236000-48236600	Enhancers	Fetal Thymus	thymus
17	chr3:48236200-48236600	Flanking Active TSS	Placenta	Placenta
18	chr3:48236200-48236600	Enhancers	HepG2	liver
19	chr3:48236400-48237400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:48236400-48237600	Weak transcription	Primary B cells from cord blood	blood
21	chr3:48236400-48237600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:48236400-48237800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:48236400-48238000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:48236400-48238000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:48236400-48238000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:48236400-48238000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:48236400-48238400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:48236400-48240000	Weak transcription	Right Atrium	heart
29	chr3:48236400-48244400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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