Variant report

Variant	rs796566
Chromosome Location	chr3:47938354-47938355
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1013431	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060407	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1061003	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130148	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs11130150	0.92[ASN][1000 genomes]
rs11130152	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130154	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1137524	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707679	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710199	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11712464	0.88[CEU][hapmap]
rs12495204	0.84[CEU][hapmap]
rs13072132	0.84[CEU][hapmap]
rs13074973	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075457	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13075795	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077230	0.92[ASN][1000 genomes]
rs13079407	0.91[CEU][hapmap]
rs13081701	0.86[EUR][1000 genomes]
rs13085054	0.91[CEU][hapmap]
rs13091913	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs13093830	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094264	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs1486915	0.88[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1530646	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550914	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1665982	0.82[EUR][1000 genomes]
rs1684942	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17079785	0.88[CEU][hapmap]
rs17290490	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs184388	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047559	0.88[CEU][hapmap]
rs2053767	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121754	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166770	0.96[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166772	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631721	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28637561	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2882668	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319680	0.82[EUR][1000 genomes]
rs319681	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319682	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319684	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319685	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319686	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319687	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319688	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319689	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319690	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs319691	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319692	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319693	0.88[CEU][hapmap];0.80[ASN][1000 genomes]
rs319694	0.92[ASN][1000 genomes]
rs319695	0.80[ASN][1000 genomes]
rs319696	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34025851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34249203	0.80[ASN][1000 genomes]
rs34448818	0.84[CEU][hapmap]
rs34750113	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35199727	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35314534	0.89[EUR][1000 genomes]
rs35582375	0.92[ASN][1000 genomes]
rs35689209	0.84[EUR][1000 genomes]
rs35943823	0.82[EUR][1000 genomes]
rs3732529	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772399	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs3888	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs3915654	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs4293721	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4296617	0.89[EUR][1000 genomes]
rs4392441	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599334	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858810	0.92[CEU][hapmap]
rs4858851	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4858860	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4858863	0.88[CEU][hapmap]
rs4858871	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858876	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858880	0.83[EUR][1000 genomes]
rs4858881	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858887	0.87[EUR][1000 genomes]
rs5012971	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60446735	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260764	0.82[EUR][1000 genomes]
rs62263575	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6442082	0.88[CEU][hapmap]
rs6442090	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442091	0.89[EUR][1000 genomes]
rs6442094	0.82[EUR][1000 genomes]
rs6442096	0.83[EUR][1000 genomes]
rs6442101	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6763824	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs6768699	0.88[CEU][hapmap]
rs6770467	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770477	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772396	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773208	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776963	0.83[CEU][hapmap]
rs6777632	0.88[CEU][hapmap]
rs6783629	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785669	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs6786001	0.88[CEU][hapmap]
rs6791834	0.85[EUR][1000 genomes]
rs6792350	0.84[AFR][1000 genomes]
rs6803741	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6806820	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806860	0.83[CEU][hapmap]
rs7374516	0.96[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7426976	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7427418	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7429990	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7430879	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7430913	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618758	0.88[CEU][hapmap]
rs7619882	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620736	0.85[EUR][1000 genomes]
rs7627645	0.87[EUR][1000 genomes]
rs7629850	0.88[CEU][hapmap]
rs7638103	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs7642590	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7645846	0.85[CEU][hapmap]
rs7649981	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653368	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777014	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs777015	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777017	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs800762	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs810334	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681917	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs9811277	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812875	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814961	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9825114	0.91[CEU][hapmap]
rs9842649	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846062	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854454	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860485	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862913	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs796566	ZNF589	cis	Nerve Tibial	GTEx
rs796566	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs796566	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs796566	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs796566	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47910200-47957000	Weak transcription	Small Intestine	intestine
2	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:47912600-47939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:47915000-47939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:47922000-47951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:47926800-47953400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:47926800-47957400	Weak transcription	Colonic Mucosa	Colon
9	chr3:47930000-47940000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:47930200-47941600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr3:47932000-47969200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:47932400-47941600	Strong transcription	HSMMtube	muscle
13	chr3:47932400-47941800	Strong transcription	NH-A	brain
14	chr3:47933000-47942800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:47933200-47943800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:47933200-47953200	Weak transcription	Fetal Kidney	kidney
17	chr3:47933800-47939000	Weak transcription	Fetal Thymus	thymus
18	chr3:47933800-47939000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:47933800-47942800	Weak transcription	Aorta	Aorta
20	chr3:47933800-47948400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:47933800-47952200	Weak transcription	Psoas Muscle	Psoas
22	chr3:47933800-47953000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:47934000-47938400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:47934000-47940800	Weak transcription	Pancreas	Pancrea
25	chr3:47934000-47941000	Weak transcription	Stomach Mucosa	stomach
26	chr3:47934000-47941200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:47934000-47941200	Weak transcription	HMEC	breast
28	chr3:47934000-47941800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:47934000-47946600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:47934000-47952400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:47934000-47952400	Weak transcription	Spleen	Spleen
32	chr3:47934000-47952800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:47934200-47941000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:47934200-47943000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:47934200-47950400	Weak transcription	HUVEC	blood vessel
36	chr3:47934200-47951000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:47934200-47952000	Weak transcription	Ovary	ovary
38	chr3:47934200-47952400	Weak transcription	Esophagus	oesophagus
39	chr3:47934200-47952600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:47934200-47953400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:47934200-47957200	Weak transcription	Gastric	stomach
42	chr3:47934400-47939200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:47934400-47939200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:47934400-47939400	Weak transcription	Dnd41	blood
45	chr3:47934400-47939400	Weak transcription	HepG2	liver
46	chr3:47934400-47940600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:47934400-47941000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:47934400-47942000	Weak transcription	Lung	lung
49	chr3:47934400-47950600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:47934400-47952200	Weak transcription	A549	lung

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