Variant report

Variant	rs9869141
Chromosome Location	chr3:113116059-113116060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10934228	0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488964	0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635786	0.86[CHB][hapmap]
rs12636607	0.86[CHB][hapmap]
rs13091945	0.83[AMR][1000 genomes]
rs17321330	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs1906142	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1979554	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2054823	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2129430	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2171293	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2895413	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35581027	0.86[EUR][1000 genomes]
rs35935366	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732806	0.86[CHB][hapmap]
rs4682138	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]
rs4682486	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438140	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438145	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438146	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438148	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66524865	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768117	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs6769970	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap]
rs6775574	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6777880	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805691	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7617772	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7618884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621210	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7623122	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];0.96[ASN][1000 genomes]
rs7623389	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625841	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7631730	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7633428	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7642163	0.84[EUR][1000 genomes]
rs7643592	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs7643843	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs7646985	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647220	0.82[TSI][hapmap]
rs7650538	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs775232	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775233	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9682734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815835	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9840124	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848087	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9866748	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9870996	0.87[YRI][hapmap]
rs9990291	0.84[AMR][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
rs9869141	WDR52	cis	parietal	SCAN
rs9869141	SIDT1	cis	parietal	SCAN

Chromatin state (count:77 , 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	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:113068400-113117000	Weak transcription	Thymus	Thymus
4	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
6	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
8	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:113081600-113121200	Weak transcription	Ovary	ovary
10	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
11	chr3:113081800-113116600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
14	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:113096600-113121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:113097800-113117800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:113098200-113117000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:113099000-113134800	Weak transcription	A549	lung
20	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:113101800-113121200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
23	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:113102800-113122600	Weak transcription	Spleen	Spleen
25	chr3:113103200-113126200	Weak transcription	Right Ventricle	heart
26	chr3:113104000-113117000	Weak transcription	Adipose Nuclei	Adipose
27	chr3:113104000-113117600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:113104000-113127400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:113105200-113122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:113105600-113124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:113106800-113117800	Weak transcription	Lung	lung
32	chr3:113106800-113122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:113106800-113143600	Weak transcription	Dnd41	blood
34	chr3:113107000-113121800	Weak transcription	Fetal Intestine Large	intestine
35	chr3:113107000-113127400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
37	chr3:113107200-113117000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:113107200-113122000	Weak transcription	Gastric	stomach
39	chr3:113107200-113124200	Weak transcription	Fetal Stomach	stomach
40	chr3:113107200-113124200	Weak transcription	GM12878-XiMat	blood
41	chr3:113107200-113124600	Weak transcription	Fetal Intestine Small	intestine
42	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
43	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:113108600-113125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:113109400-113121800	Weak transcription	Fetal Lung	lung
47	chr3:113110200-113117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:113110200-113124400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:113110400-113117600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:113110600-113121200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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