Variant report

Variant	rs12635786
Chromosome Location	chr3:113135345-113135346
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10934229	0.82[MEX][hapmap]
rs10934231	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11923005	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233528	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630518	0.82[MEX][hapmap]
rs12636607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1353903	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs1392284	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1463640	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs2129433	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2270781	0.82[MEX][hapmap]
rs2291413	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3732806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732808	0.85[LWK][hapmap]
rs4682134	0.82[ASN][1000 genomes]
rs4682136	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4682138	0.87[CHB][hapmap]
rs55710804	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56339567	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60329418	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6438143	0.86[CHB][hapmap]
rs6438144	0.87[CHB][hapmap]
rs6438147	0.87[CHB][hapmap]
rs6768117	0.87[CHB][hapmap]
rs6779002	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6779305	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237136	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237142	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237146	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239111	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239117	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239120	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73239121	0.90[AMR][1000 genomes]
rs7623122	0.87[CHB][hapmap]
rs7625933	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630301	0.82[ASN][1000 genomes]
rs7638599	0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9857471	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9869141	0.86[CHB][hapmap]
rs9872143	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv822221	chr3:113135096-113135541	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12635786	WDR52	cis	cerebellum	SCAN
rs12635786	BOC	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:113106800-113143600	Weak transcription	Dnd41	blood
7	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
8	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
9	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
15	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
16	chr3:113119600-113145200	Weak transcription	Lung	lung
17	chr3:113122400-113138400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:113122400-113144800	Weak transcription	Pancreas	Pancrea
19	chr3:113122800-113138000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:113122800-113138600	Weak transcription	Primary B cells from cord blood	blood
21	chr3:113122800-113144000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:113122800-113144000	Weak transcription	Thymus	Thymus
23	chr3:113122800-113144800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:113123000-113143600	Weak transcription	Left Ventricle	heart
25	chr3:113123000-113144400	Weak transcription	HSMM	muscle
26	chr3:113123200-113143800	Weak transcription	Ovary	ovary
27	chr3:113123600-113143200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:113124600-113143600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:113125000-113138000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:113129000-113142600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:113132600-113146400	Weak transcription	Right Ventricle	heart
32	chr3:113132800-113137800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:113133200-113147800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:113133400-113138600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:113133400-113144600	Weak transcription	NH-A	brain
36	chr3:113133600-113135400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:113133600-113135400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:113133800-113135400	Strong transcription	Liver	Liver
39	chr3:113134000-113135400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:113134000-113138600	Weak transcription	GM12878-XiMat	blood
41	chr3:113134000-113144000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:113134000-113144400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:113134200-113135400	Strong transcription	Fetal Kidney	kidney
44	chr3:113134200-113135600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:113134200-113136000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:113134200-113137600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:113134200-113143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:113134400-113135400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:113134400-113135400	Strong transcription	Adipose Nuclei	Adipose
50	chr3:113134400-113137000	Weak transcription	Fetal Stomach	stomach

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