Variant report

Variant	rs564971
Chromosome Location	chr1:92600090-92600091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10783109	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875204	0.90[ASN][1000 genomes]
rs10875209	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875214	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875237	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11166141	0.90[ASN][1000 genomes]
rs11166144	0.90[ASN][1000 genomes]
rs11166184	0.90[ASN][1000 genomes]
rs11166218	0.84[EUR][1000 genomes]
rs1157469	0.84[EUR][1000 genomes]
rs1157470	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119246	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1226176	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226179	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226183	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226187	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759512	0.82[EUR][1000 genomes]
rs1384612	0.84[EUR][1000 genomes]
rs1384613	0.84[EUR][1000 genomes]
rs1601020	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1601021	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1601023	0.90[ASN][1000 genomes]
rs17519385	0.84[EUR][1000 genomes]
rs17578686	0.84[EUR][1000 genomes]
rs1982720	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069051	0.84[EUR][1000 genomes]
rs2093879	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2128645	0.90[ASN][1000 genomes]
rs2181897	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209337	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391114	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391116	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839877	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893200	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35015161	0.84[EUR][1000 genomes]
rs3851271	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851272	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851273	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261159	0.90[ASN][1000 genomes]
rs4437922	0.90[ASN][1000 genomes]
rs4623754	0.90[ASN][1000 genomes]
rs4658127	0.90[ASN][1000 genomes]
rs4658128	0.90[ASN][1000 genomes]
rs4658129	0.90[ASN][1000 genomes]
rs4658290	0.90[ASN][1000 genomes]
rs4658291	0.90[ASN][1000 genomes]
rs4658294	0.85[EUR][1000 genomes]
rs488288	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488849	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490800	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492164	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493595	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504606	0.83[EUR][1000 genomes]
rs504613	0.83[EUR][1000 genomes]
rs506375	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506377	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs507452	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511546	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515280	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519343	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519623	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519932	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527412	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529135	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534547	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539288	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544557	0.86[EUR][1000 genomes]
rs547699	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551909	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553861	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556980	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs560389	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563113	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563606	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569178	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569593	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569962	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs570368	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs573044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604080	0.86[EUR][1000 genomes]
rs6677184	0.90[ASN][1000 genomes]
rs6684317	0.90[ASN][1000 genomes]
rs7511656	0.80[EUR][1000 genomes]
rs7522081	0.80[EUR][1000 genomes]
rs7533077	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7537221	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541482	0.90[ASN][1000 genomes]
rs7542358	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7542373	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545076	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549158	0.85[ASN][1000 genomes]
rs9661633	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981583	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv871948	chr1:92574745-92607997	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3446549	chr1:92596110-92610495	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92552600-92613400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:92552800-92613600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:92555200-92620400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:92556000-92613600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:92556600-92613400	Weak transcription	Fetal Brain Female	brain
6	chr1:92558000-92604000	Weak transcription	Left Ventricle	heart
7	chr1:92560000-92613600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:92561200-92619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:92567200-92624200	Weak transcription	Fetal Stomach	stomach
10	chr1:92567400-92618000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:92568200-92616400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:92569800-92613600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:92570000-92619600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:92571800-92601600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:92571800-92613400	Weak transcription	Dnd41	blood
16	chr1:92572000-92613400	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:92574000-92613400	Weak transcription	Fetal Lung	lung
18	chr1:92580800-92615200	Weak transcription	Lung	lung
19	chr1:92580800-92619000	Weak transcription	Pancreas	Pancrea
20	chr1:92581400-92613600	Weak transcription	Liver	Liver
21	chr1:92586000-92613400	Weak transcription	Esophagus	oesophagus
22	chr1:92586400-92601600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:92589600-92600200	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:92590200-92613400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:92590200-92624400	Weak transcription	Psoas Muscle	Psoas
26	chr1:92591200-92613000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:92591200-92613600	Weak transcription	Aorta	Aorta
28	chr1:92591200-92615200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:92594000-92601600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:92594000-92613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:92594000-92618200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:92595000-92601800	Weak transcription	Fetal Brain Male	brain
33	chr1:92596000-92601600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:92596200-92614000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:92596600-92615200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:92596600-92616600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:92596800-92607400	Weak transcription	Adipose Nuclei	Adipose
38	chr1:92597600-92621000	Weak transcription	Fetal Intestine Small	intestine
39	chr1:92597800-92616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:92598000-92613400	Weak transcription	Brain Substantia Nigra	brain
41	chr1:92598400-92613400	Weak transcription	Ovary	ovary
42	chr1:92598400-92619400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:92598600-92613800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:92599200-92603600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:92599200-92613200	Weak transcription	Primary T cells from cord blood	blood
46	chr1:92599200-92613600	Weak transcription	Fetal Intestine Large	intestine
47	chr1:92599800-92600200	Enhancers	Fetal Kidney	kidney

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