Variant report

Variant	rs11706189
Chromosome Location	chr3:49210833-49210834
allele	A/C
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	NFIC	chr3:49210685-49211332	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
2	MEF2A	chr3:49210715-49211082	K562	blood:	n/a	chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
3	REST	chr3:49210812-49211590	SK-N-SH	brain:	n/a	n/a
4	REST	chr3:49210427-49211993	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:49210676-49211201	H1-neurons	neurons:	n/a	n/a
6	MEF2A	chr3:49210626-49211078	K562	blood:	n/a	chr3:49210627-49210635 chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
7	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
8	POLR2A	chr3:49210721-49211608	H1-neurons	neurons:	n/a	n/a
9	NFIC	chr3:49210601-49211651	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
10	TBL1XR1	chr3:49210624-49211122	K562	blood:	n/a	n/a
11	EP300	chr3:49210750-49211254	SK-N-SH_RA	brain:	n/a	n/a
12	RCOR1	chr3:49210776-49211213	K562	blood:	n/a	n/a
13	RAD21	chr3:49210791-49211644	SK-N-SH_RA	brain:	n/a	chr3:49211373-49211386 chr3:49211355-49211364
14	ZMIZ1	chr3:49210797-49210910	K562	blood:	n/a	n/a
15	EP300	chr3:49210783-49211182	K562	blood:	n/a	n/a
16	SP1	chr3:49210801-49211194	H1-hESC	embryonic stem cell:	n/a	chr3:49210952-49210961 chr3:49210952-49210966 chr3:49210951-49210962 chr3:49210952-49210962 chr3:49210953-49210962 chr3:49210952-49210962
17	NR2F2	chr3:49210558-49211119	K562	blood:	n/a	n/a
18	MAZ	chr3:49210763-49211124	K562	blood:	n/a	chr3:49211021-49211030
19	EP300	chr3:49210709-49211171	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

Variant related genes	Relation type
KLHDC8B	TF binding region
ENSG00000172037	Chromatin interaction
ENSG00000270441	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000185909	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865954	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11130182	0.88[ASN][1000 genomes]
rs11130184	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1134043	0.92[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11710247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715581	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11716334	0.87[ASN][1000 genomes]
rs11716445	0.92[CEU][hapmap]
rs11716614	0.92[CEU][hapmap]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12493001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12629759	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12631989	1.00[JPT][hapmap]
rs12636030	1.00[ASN][1000 genomes]
rs12637576	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12715434	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.85[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2117938	1.00[JPT][hapmap]
rs2304442	1.00[JPT][hapmap]
rs3212	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.81[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102816	0.84[EUR][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35174559	1.00[JPT][hapmap]
rs35185152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4308307	0.92[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.97[ASN][1000 genomes]
rs4513485	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4521268	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4536858	0.97[ASN][1000 genomes]
rs4955410	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4955418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955420	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974080	1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55713230	0.97[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs6414613	1.00[JPT][hapmap]
rs6446205	1.00[JPT][hapmap]
rs66991555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67286839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6779394	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6781790	1.00[JPT][hapmap]
rs67831908	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6790914	0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324939	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.92[EUR][1000 genomes]
rs7615235	0.82[ASN][1000 genomes]
rs7621015	1.00[JPT][hapmap]
rs7626445	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826525	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	0.85[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap]
rs9846123	1.00[JPT][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850917	1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9855123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11706189	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs11706189	WDR6	cis	Esophagus Mucosa	GTEx
rs11706189	WDR6	cis	Artery Tibial	GTEx
rs11706189	WDR6	cis	Adipose Subcutaneous	GTEx
rs11706189	WDR6	cis	Whole Blood	GTEx
rs11706189	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49208200-49211200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:49208200-49211400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:49208200-49212000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:49209200-49211800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49209200-49212000	Flanking Active TSS	Fetal Brain Female	brain
6	chr3:49209200-49212400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:49209400-49211200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:49209400-49211200	Flanking Active TSS	K562	blood
9	chr3:49209400-49211400	Flanking Active TSS	HepG2	liver
10	chr3:49209400-49211600	Flanking Active TSS	Fetal Lung	lung
11	chr3:49209400-49211600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:49209600-49211000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr3:49209600-49211000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:49209600-49211200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:49209600-49211400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49209600-49211400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:49209600-49211400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr3:49209600-49211600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:49209600-49211600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:49209600-49211800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
21	chr3:49209600-49211800	Flanking Active TSS	HSMMtube	muscle
22	chr3:49209600-49212000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:49209600-49212000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
24	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:49209800-49211200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:49209800-49211200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:49209800-49211200	Flanking Active TSS	HSMM	muscle
28	chr3:49209800-49211400	Flanking Active TSS	Left Ventricle	heart
29	chr3:49209800-49211400	Flanking Active TSS	Right Ventricle	heart
30	chr3:49209800-49212000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:49209800-49212400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:49209800-49212600	Enhancers	Fetal Brain Male	brain
33	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:49210000-49211000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:49210000-49211200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:49210000-49211200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:49210000-49211400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:49210000-49211400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
39	chr3:49210000-49211400	Enhancers	Brain Substantia Nigra	brain
40	chr3:49210000-49211600	Weak transcription	Primary T cells from cord blood	blood
41	chr3:49210000-49211600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:49210000-49211600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:49210000-49211600	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr3:49210000-49211600	Flanking Active TSS	Right Atrium	heart
45	chr3:49210000-49211800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr3:49210000-49211800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
47	chr3:49210000-49211800	Enhancers	Placenta	Placenta
48	chr3:49210000-49211800	Flanking Active TSS	Ovary	ovary
49	chr3:49210000-49212000	Enhancers	Osteobl	bone
50	chr3:49210000-49212800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland

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