Variant report

Variant	rs1392284
Chromosome Location	chr3:113101410-113101411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11923005	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12233528	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12635786	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]
rs12636607	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1353903	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1463640	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2129433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171293	0.87[CHB][hapmap]
rs3732806	0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682134	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779002	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779305	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73235093	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73237136	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73237142	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73239120	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625933	0.84[ASN][1000 genomes]
rs7630301	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7632821	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7638599	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653187	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9682734	0.87[CHB][hapmap]
rs9820386	0.84[MEX][hapmap];0.80[TSI][hapmap]
rs9857471	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9872143	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1392284	WDR52	cis	cerebellum	SCAN
rs1392284	SLC35A5	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113066200-113102800	Weak transcription	Aorta	Aorta
4	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:113068400-113117000	Weak transcription	Thymus	Thymus
6	chr3:113069000-113101800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
9	chr3:113077800-113102400	Weak transcription	HSMM	muscle
10	chr3:113078600-113109800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:113080000-113114200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
14	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:113081600-113103400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:113081600-113104400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:113081600-113105600	Weak transcription	Esophagus	oesophagus
18	chr3:113081600-113105800	Weak transcription	Gastric	stomach
19	chr3:113081600-113106200	Weak transcription	Lung	lung
20	chr3:113081600-113121200	Weak transcription	Ovary	ovary
21	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
22	chr3:113081800-113116600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:113082200-113113200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:113086200-113105800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:113086200-113106400	Weak transcription	Fetal Stomach	stomach
26	chr3:113090800-113106600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:113091800-113104600	Weak transcription	NH-A	brain
29	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
30	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:113094200-113108800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:113096200-113105600	Weak transcription	Liver	Liver
33	chr3:113096400-113106600	Weak transcription	GM12878-XiMat	blood
34	chr3:113096600-113121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:113097400-113101800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:113097600-113103600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:113097800-113105800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:113097800-113117800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:113098200-113117000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:113099000-113104000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:113099000-113134800	Weak transcription	A549	lung
43	chr3:113099400-113106800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:113099400-113113400	Weak transcription	Left Ventricle	heart
45	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:113099800-113102000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:113099800-113103400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:113099800-113106200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:113099800-113106800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:113100000-113103200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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