Variant report

Variant	rs4682138
Chromosome Location	chr3:113150806-113150807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10934228	0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs11715198	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488964	0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635786	0.87[CHB][hapmap]
rs12636607	0.86[CHB][hapmap]
rs17321330	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1906142	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979554	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2054823	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2129430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171293	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2895413	0.87[EUR][1000 genomes]
rs35581027	0.83[EUR][1000 genomes]
rs35935366	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732806	0.87[CHB][hapmap]
rs4682486	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438140	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438144	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438145	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438146	0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66524865	0.86[EUR][1000 genomes]
rs6767932	0.81[AMR][1000 genomes]
rs6768117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769970	0.82[CHB][hapmap]
rs6775574	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6777880	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6783773	0.81[AMR][1000 genomes]
rs6805691	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7617772	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7618884	0.87[EUR][1000 genomes]
rs7621210	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7623122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7623389	0.86[EUR][1000 genomes]
rs7625841	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7631730	0.86[EUR][1000 genomes]
rs7633428	0.86[EUR][1000 genomes]
rs7642163	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7643592	0.81[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7643843	0.81[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7646985	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7647220	0.82[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs7650538	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7653186	0.81[CEU][hapmap]
rs775232	0.86[EUR][1000 genomes]
rs775233	0.87[EUR][1000 genomes]
rs9682734	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs9815835	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9840124	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9848087	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866748	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9869141	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4682138	WDR52	cis	parietal	SCAN
rs4682138	SIDT1	cis	parietal	SCAN
rs4682138	SIDT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:113137400-113160000	Weak transcription	Fetal Stomach	stomach
7	chr3:113140000-113160000	Weak transcription	Psoas Muscle	Psoas
8	chr3:113144200-113151400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:113145800-113155800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:113145800-113159400	Weak transcription	Gastric	stomach
11	chr3:113145800-113159400	Weak transcription	HSMMtube	muscle
12	chr3:113145800-113159600	Weak transcription	Lung	lung
13	chr3:113145800-113159800	Weak transcription	Esophagus	oesophagus
14	chr3:113145800-113159800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:113145800-113159800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:113145800-113159800	Weak transcription	Thymus	Thymus
17	chr3:113145800-113160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:113145800-113160200	Weak transcription	Aorta	Aorta
19	chr3:113145800-113166000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:113145800-113176600	Weak transcription	Spleen	Spleen
21	chr3:113146000-113154200	Weak transcription	Fetal Thymus	thymus
22	chr3:113146000-113155400	Weak transcription	Osteobl	bone
23	chr3:113146000-113155800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:113146000-113159800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:113146000-113160000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:113146000-113160000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:113146000-113160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:113146000-113172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:113146200-113153000	Weak transcription	Colonic Mucosa	Colon
31	chr3:113146200-113155400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:113146200-113159600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:113146200-113159600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:113146200-113159600	Weak transcription	Dnd41	blood
35	chr3:113146200-113160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:113146200-113160000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:113146200-113160200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:113146200-113178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:113146400-113159000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:113146400-113160000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:113146400-113165000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:113146800-113155400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:113147000-113159800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:113147000-113159800	Weak transcription	Adipose Nuclei	Adipose
45	chr3:113147000-113165600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:113147200-113154600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:113147200-113155400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:113147200-113159400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:113147200-113159600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:113147200-113160200	Weak transcription	Primary hematopoietic stem cells	blood

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