Variant report

Variant	rs12749317
Chromosome Location	chr1:92747329-92747330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10874637	0.88[EUR][1000 genomes]
rs10875319	0.90[ASN][1000 genomes]
rs11164226	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164312	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11577572	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11578012	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11578400	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11580693	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585255	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11586355	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11586989	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11588044	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588153	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589858	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12094293	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12401372	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404806	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406749	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407622	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12411162	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727665	0.89[ASN][1000 genomes]
rs12731923	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12735898	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12740246	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12755781	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12757533	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12759512	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1384612	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1384613	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1487540	0.90[ASN][1000 genomes]
rs17519385	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17578686	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1809606	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2004814	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2046620	0.90[ASN][1000 genomes]
rs2069051	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2087194	0.90[ASN][1000 genomes]
rs2391158	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391162	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3103176	0.90[ASN][1000 genomes]
rs3103181	0.90[ASN][1000 genomes]
rs3122321	0.90[ASN][1000 genomes]
rs3122327	0.81[ASN][1000 genomes]
rs3131813	0.90[ASN][1000 genomes]
rs3131827	0.90[ASN][1000 genomes]
rs3131828	0.90[ASN][1000 genomes]
rs34090353	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015161	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35580949	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658294	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4658297	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658298	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658299	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949888	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970699	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970713	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6603973	0.86[EUR][1000 genomes]
rs6662379	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662920	0.82[EUR][1000 genomes]
rs6663905	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66758257	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720457	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7522081	0.82[EUR][1000 genomes]
rs7524120	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550680	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9439911	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92710600-92753200	Weak transcription	Small Intestine	intestine
4	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
5	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:92710600-92764000	Weak transcription	Gastric	stomach
7	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
8	chr1:92711200-92761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
10	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
11	chr1:92719600-92760800	Weak transcription	Fetal Heart	heart
12	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:92720400-92748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:92724000-92760600	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
18	chr1:92724800-92747400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:92725800-92764000	Weak transcription	Colonic Mucosa	Colon
20	chr1:92727000-92763800	Weak transcription	Right Ventricle	heart
21	chr1:92727200-92759200	Weak transcription	A549	lung
22	chr1:92727200-92763800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:92729800-92763800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:92731400-92751200	Weak transcription	GM12878-XiMat	blood
25	chr1:92732000-92750800	Weak transcription	Fetal Kidney	kidney
26	chr1:92732000-92763600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:92733000-92749200	Strong transcription	Fetal Thymus	thymus
28	chr1:92733600-92754800	Weak transcription	HMEC	breast
29	chr1:92735200-92752400	Weak transcription	Psoas Muscle	Psoas
30	chr1:92736000-92763600	Weak transcription	Liver	Liver
31	chr1:92736800-92763800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:92737200-92747400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:92737800-92759400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:92738000-92760600	Weak transcription	Hela-S3	cervix
35	chr1:92738000-92763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:92738400-92752200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:92738400-92763800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:92738800-92763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:92739800-92751000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:92740000-92747400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:92740800-92752400	Weak transcription	HSMM	muscle
42	chr1:92741000-92754400	Weak transcription	K562	blood
43	chr1:92741400-92754000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:92742200-92754600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:92742400-92753600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:92742600-92750800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:92742800-92750800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:92743200-92750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:92743200-92753600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:92743200-92759200	Weak transcription	NHLF	lung

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