Variant report

Variant	rs488288
Chromosome Location	chr1:92574731-92574732
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10783109	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875204	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875209	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875214	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875237	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11166141	0.90[ASN][1000 genomes]
rs11166144	0.90[ASN][1000 genomes]
rs11166184	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11166218	0.80[EUR][1000 genomes]
rs1157469	0.81[EUR][1000 genomes]
rs1157470	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119246	0.90[ASN][1000 genomes]
rs1226176	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226179	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226183	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226187	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384612	0.81[EUR][1000 genomes]
rs1384613	0.81[EUR][1000 genomes]
rs1601020	0.90[ASN][1000 genomes]
rs1601021	0.90[ASN][1000 genomes]
rs1601023	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17519385	0.81[EUR][1000 genomes]
rs17578686	0.81[EUR][1000 genomes]
rs1982720	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069051	0.81[EUR][1000 genomes]
rs2093879	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2128645	0.90[ASN][1000 genomes]
rs2181897	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209337	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391114	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391116	0.90[ASN][1000 genomes]
rs2839877	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893200	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35015161	0.81[EUR][1000 genomes]
rs3851271	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851272	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851273	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261159	0.90[ASN][1000 genomes]
rs4437922	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4623754	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658127	0.90[ASN][1000 genomes]
rs4658128	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658129	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658290	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658291	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658294	0.83[EUR][1000 genomes]
rs488849	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490800	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492164	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493595	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506375	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506377	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs507452	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511546	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515280	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519343	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519623	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519932	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527412	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529135	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539288	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544557	0.83[EUR][1000 genomes]
rs547699	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551909	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553861	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556980	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs560389	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563113	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563606	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564971	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569178	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569593	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569962	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs570368	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs573044	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575805	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604080	0.85[EUR][1000 genomes]
rs6677184	0.90[ASN][1000 genomes]
rs6684317	0.90[ASN][1000 genomes]
rs7533077	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7537221	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541482	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7542358	0.90[ASN][1000 genomes]
rs7542373	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545076	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549158	0.85[ASN][1000 genomes]
rs7549516	0.81[EUR][1000 genomes]
rs9661633	0.85[ASN][1000 genomes]
rs981583	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS 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	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers 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	15 gene(s)	inside rSNPs	diseases
12	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	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
19	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv871415	chr1:92340684-92641607	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	esv2750842	chr1:92356781-92579675	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv871144	chr1:92380302-92641607	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	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
24	nsv1009079	chr1:92525630-92595669	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv546821	chr1:92525678-92650349	ZNF genes & repeats Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
26	nsv870471	chr1:92568263-92604114	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92552000-92577400	Weak transcription	Fetal Brain Male	brain
2	chr1:92552200-92580400	Weak transcription	Aorta	Aorta
3	chr1:92552200-92583800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:92552400-92586000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:92552400-92595200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:92552600-92579200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:92552600-92582400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:92552600-92590000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:92552600-92591600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:92552600-92613400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:92552800-92579000	Weak transcription	Psoas Muscle	Psoas
12	chr1:92552800-92613600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:92553200-92576600	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:92553800-92575800	Weak transcription	Fetal Kidney	kidney
15	chr1:92554400-92583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:92555200-92580400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:92555200-92620400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:92555400-92580400	Weak transcription	Ovary	ovary
19	chr1:92555800-92576000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:92556000-92613600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:92556600-92613400	Weak transcription	Fetal Brain Female	brain
22	chr1:92557400-92598000	Weak transcription	Spleen	Spleen
23	chr1:92558000-92583000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:92558000-92604000	Weak transcription	Left Ventricle	heart
25	chr1:92560000-92613600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:92560400-92580400	Weak transcription	Lung	lung
27	chr1:92560600-92590800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:92561200-92619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:92561600-92590000	Weak transcription	Brain Substantia Nigra	brain
30	chr1:92562600-92582800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:92562800-92575000	Weak transcription	Primary T cells from cord blood	blood
32	chr1:92565600-92575200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:92565600-92583000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:92567200-92624200	Weak transcription	Fetal Stomach	stomach
35	chr1:92567400-92618000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:92567600-92580400	Weak transcription	Pancreas	Pancrea
37	chr1:92567600-92581600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:92567800-92577400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:92568000-92583200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:92568200-92616400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:92568600-92577600	Weak transcription	Gastric	stomach
42	chr1:92569400-92595600	Weak transcription	Brain Germinal Matrix	brain
43	chr1:92569600-92583000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:92569800-92578000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:92569800-92613600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:92570000-92619600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:92570400-92589400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:92570800-92594800	Weak transcription	Fetal Intestine Large	intestine
49	chr1:92571800-92601600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:92571800-92613400	Weak transcription	Dnd41	blood

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