Variant report

Variant	rs11707606
Chromosome Location	chr3:48237087-48237088
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48235629..48237322-chr3:48585256..48587869,2	K562	blood:
2	chr3:48235629..48237555-chr3:48585079..48587869,3	K562	blood:
3	chr3:48228787..48232242-chr3:48236568..48239852,3	K562	blood:

Variant related genes	Relation type
ENSG00000114268	Chromatin interaction
ENSG00000164045	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]
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]
rs3731489	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: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
rs11707606	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs11707606	ZNF589	cis	Nerve Tibial	GTEx
rs11707606	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11707606	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs11707606	NME6	cis	Muscle Skeletal	GTEx
rs11707606	ZNF589	cis	Thyroid	GTEx
rs11707606	MRPS18AP1	cis	Stomach	GTEx
rs11707606	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs11707606	NME6	cis	Nerve Tibial	GTEx
rs11707606	NME6	cis	Artery Tibial	GTEx
rs11707606	CDC25A	cis	Thyroid	GTEx
rs11707606	ZNF589	cis	Artery Aorta	GTEx
rs11707606	NME6	cis	multi-tissue	Pritchard
rs11707606	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11707606	ZNF589	cis	Adipose Subcutaneous	GTEx
rs11707606	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs11707606	ZNF589	cis	Stomach	GTEx
rs11707606	CDC25A	cis	Artery Tibial	GTEx
rs11707606	MRPS18AP1	cis	Artery Tibial	GTEx
rs11707606	ZNF589	cis	Esophagus Muscularis	GTEx
rs11707606	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs11707606	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs11707606	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs11707606	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs11707606	SPINK8	cis	Whole Blood	GTEx
rs11707606	CDC25A	cis	Muscle Skeletal	GTEx
rs11707606	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11707606	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs11707606	MRPS18AP1	cis	Thyroid	GTEx
rs11707606	MRPS18AP1	cis	lung	GTEx
rs11707606	FCF1P2	cis	Artery Tibial	GTEx
rs11707606	ZNF589	cis	Esophagus Mucosa	GTEx
rs11707606	NME6	cis	Esophagus Muscularis	GTEx
rs11707606	MRPS18AP1	cis	Artery Aorta	GTEx
rs11707606	CDC25A	cis	Adipose Subcutaneous	GTEx
rs11707606	ZNF589	cis	Artery Tibial	GTEx
rs11707606	ZNF589	cis	lung	GTEx

Chromatin state (count:24 , 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	chr3:48235800-48237800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:48236400-48237400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:48236400-48237600	Weak transcription	Primary B cells from cord blood	blood
13	chr3:48236400-48237600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:48236400-48237800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:48236400-48238000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:48236400-48238000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:48236400-48238000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:48236400-48238000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:48236400-48238400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:48236400-48240000	Weak transcription	Right Atrium	heart
21	chr3:48236400-48244400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:48236600-48237200	Enhancers	Placenta	Placenta
23	chr3:48236600-48237800	Weak transcription	GM12878-XiMat	blood
24	chr3:48236600-48238400	Weak transcription	Fetal Thymus	thymus

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