Variant report

Variant	rs556980
Chromosome Location	chr1:92640497-92640498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91966529..91968334-chr1:92639534..92641055,2	K562	blood:

Variant related genes	Relation type
ENSG00000097046	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1014415	1.00[JPT][hapmap]
rs10158958	0.80[EUR][1000 genomes]
rs10159094	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1023041	1.00[JPT][hapmap]
rs10747503	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875209	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10875214	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10875237	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875319	1.00[JPT][hapmap]
rs10875349	1.00[JPT][hapmap]
rs11165984	1.00[JPT][hapmap]
rs11166042	1.00[JPT][hapmap]
rs11166141	1.00[JPT][hapmap]
rs11166144	1.00[JPT][hapmap]
rs1157469	0.87[CEU][hapmap]
rs1157470	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs11577572	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11585255	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588044	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588153	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs11589858	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12119246	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1226176	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226179	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226187	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12404806	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12407622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12724638	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12729867	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12734478	0.87[CEU][hapmap]
rs12740246	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12753920	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12755781	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12759512	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384612	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384613	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466514	0.83[EUR][1000 genomes]
rs1483022	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1487536	1.00[JPT][hapmap]
rs1487540	1.00[JPT][hapmap]
rs1542685	1.00[JPT][hapmap]
rs1601020	0.80[EUR][1000 genomes]
rs1601021	0.80[EUR][1000 genomes]
rs17519385	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17519972	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17578686	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872007	1.00[JPT][hapmap]
rs1982720	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2046620	1.00[JPT][hapmap]
rs2069051	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2087194	1.00[JPT][hapmap]
rs2093879	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2128645	1.00[JPT][hapmap]
rs2128646	1.00[JPT][hapmap]
rs2181897	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391114	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2391116	0.80[EUR][1000 genomes]
rs2839877	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2893200	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3103176	1.00[JPT][hapmap]
rs3103178	1.00[JPT][hapmap]
rs3103181	1.00[JPT][hapmap]
rs3118137	0.90[ASN][1000 genomes]
rs3131814	1.00[JPT][hapmap]
rs3131828	1.00[JPT][hapmap]
rs35015161	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851271	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs3851272	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3851273	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4437922	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4658128	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4658290	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs4658294	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4658297	0.81[AFR][1000 genomes]
rs4658298	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs4658299	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs4658300	1.00[JPT][hapmap]
rs488288	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488849	0.84[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs490800	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs492164	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493595	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4949888	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs504606	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs504613	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs504706	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs506375	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506377	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs507452	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs511546	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs515280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519343	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519623	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527412	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs529135	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs534547	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs539288	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544557	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs547699	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551909	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs553861	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs560389	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563113	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563606	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs564971	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569178	0.89[ASN][1000 genomes]
rs569593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573044	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs575805	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6603962	1.00[JPT][hapmap]
rs6604080	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6604082	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6604090	1.00[JPT][hapmap]
rs6663278	1.00[JPT][hapmap]
rs6684317	1.00[JPT][hapmap]
rs6699855	1.00[JPT][hapmap]
rs6702267	1.00[JPT][hapmap]
rs7511656	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7511669	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520275	1.00[JPT][hapmap]
rs7522081	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7529835	0.81[ASN][1000 genomes]
rs7533077	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7537221	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542358	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7542373	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7545076	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs981583	0.84[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92609800-92651200	Weak transcription	Fetal Kidney	kidney
2	chr1:92613400-92645400	Weak transcription	Gastric	stomach
3	chr1:92615600-92646000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:92620600-92646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:92620800-92645800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:92621000-92646800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:92625000-92646800	Weak transcription	Pancreas	Pancrea
8	chr1:92625000-92648200	Weak transcription	Fetal Stomach	stomach
9	chr1:92625400-92642600	Weak transcription	Fetal Lung	lung
10	chr1:92625600-92651000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:92626200-92642600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:92626200-92646000	Weak transcription	Psoas Muscle	Psoas
13	chr1:92626200-92652000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:92626400-92643000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:92626400-92644200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:92626600-92644000	Weak transcription	Liver	Liver
17	chr1:92626600-92648400	Weak transcription	Fetal Intestine Small	intestine
18	chr1:92626600-92650800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:92626600-92657400	Weak transcription	Right Ventricle	heart
20	chr1:92626800-92646600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:92626800-92650000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:92626800-92651400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:92627800-92648200	Weak transcription	Lung	lung
24	chr1:92628000-92643200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:92628000-92645800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:92628000-92645800	Weak transcription	Left Ventricle	heart
27	chr1:92628000-92646000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:92628000-92648600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:92628200-92642600	Weak transcription	Adipose Nuclei	Adipose
30	chr1:92628200-92645800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:92628200-92645800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:92628200-92646000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:92628200-92651800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:92628400-92645800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:92628400-92646800	Weak transcription	Aorta	Aorta
36	chr1:92632800-92648800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:92633800-92649400	Weak transcription	HSMMtube	muscle
38	chr1:92634200-92645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:92634600-92641400	Weak transcription	Brain Substantia Nigra	brain
40	chr1:92634600-92647200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:92635200-92650400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:92635400-92646200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:92635600-92648400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:92635800-92645800	Weak transcription	Brain Anterior Caudate	brain
45	chr1:92636000-92642400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:92636000-92645800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:92636000-92646000	Weak transcription	Fetal Brain Male	brain
48	chr1:92636200-92651000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:92636400-92642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:92636800-92652400	Weak transcription	Fetal Brain Female	brain

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