Variant report

Variant	rs10934229
Chromosome Location	chr3:113146697-113146698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113146276..113148962-chr3:113155002..113157279,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10934230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934231	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10934233	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12054036	0.83[EUR][1000 genomes]
rs12629271	0.88[ASN][1000 genomes]
rs12629498	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12630518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632492	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12635786	0.82[MEX][hapmap]
rs12636959	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12637924	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1463644	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16860850	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16860868	0.91[EUR][1000 genomes]
rs16860899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17882622	0.81[ASN][1000 genomes]
rs2270781	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2291413	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2306069	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2399481	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28662393	0.80[ASN][1000 genomes]
rs34965320	0.81[ASN][1000 genomes]
rs3732804	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682133	0.81[ASN][1000 genomes]
rs4682136	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682485	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682489	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55667700	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55710804	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55748551	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55757335	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55865352	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55973292	0.89[EUR][1000 genomes]
rs56339567	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60292736	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60329418	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62265992	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62265996	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438142	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6809516	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs73235041	0.89[EUR][1000 genomes]
rs73235059	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73235065	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73235066	0.81[ASN][1000 genomes]
rs73235068	0.81[ASN][1000 genomes]
rs73237104	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73237110	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73237123	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73237130	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73237143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73237146	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73239107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73239111	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73239117	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73239121	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73239126	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs763805	0.90[EUR][1000 genomes]
rs7643592	0.87[CHB][hapmap]
rs7643843	0.87[CHB][hapmap]
rs7647220	0.83[CHB][hapmap]
rs7653186	0.87[CHB][hapmap]
rs8179926	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9820386	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9822309	0.81[ASN][1000 genomes]
rs9844111	0.80[ASN][1000 genomes]
rs9852204	0.81[ASN][1000 genomes]
rs9857414	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9863193	0.81[ASN][1000 genomes]
rs9878805	0.81[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10934229	WDR52	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
6	chr3:113133200-113147800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:113137400-113148600	Weak transcription	Small Intestine	intestine
11	chr3:113137400-113160000	Weak transcription	Fetal Stomach	stomach
12	chr3:113140000-113160000	Weak transcription	Psoas Muscle	Psoas
13	chr3:113141400-113147800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:113143000-113147400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:113143200-113146800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:113143400-113147200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr3:113143400-113147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:113143400-113147600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:113143600-113146800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr3:113143600-113147200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:113143600-113148000	Strong transcription	Left Ventricle	heart
22	chr3:113143800-113147000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr3:113143800-113147400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:113143800-113147800	Strong transcription	Ovary	ovary
25	chr3:113144000-113147000	Strong transcription	Adipose Nuclei	Adipose
26	chr3:113144000-113147400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:113144200-113151400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:113144400-113147600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr3:113145000-113147600	Strong transcription	A549	lung
30	chr3:113145800-113147200	Weak transcription	HUVEC	blood vessel
31	chr3:113145800-113147400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:113145800-113147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:113145800-113147400	Weak transcription	Pancreas	Pancrea
34	chr3:113145800-113147400	Weak transcription	HSMM	muscle
35	chr3:113145800-113147600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:113145800-113147600	Strong transcription	Primary T cells from cord blood	blood
37	chr3:113145800-113147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:113145800-113149000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:113145800-113149800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:113145800-113150200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:113145800-113155800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:113145800-113159400	Weak transcription	Gastric	stomach
43	chr3:113145800-113159400	Weak transcription	HSMMtube	muscle
44	chr3:113145800-113159600	Weak transcription	Lung	lung
45	chr3:113145800-113159800	Weak transcription	Esophagus	oesophagus
46	chr3:113145800-113159800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:113145800-113159800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:113145800-113159800	Weak transcription	Thymus	Thymus
49	chr3:113145800-113160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:113145800-113160200	Weak transcription	Aorta	Aorta

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