Variant report

Variant	rs10889292
Chromosome Location	chr1:62618748-62618749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10789103	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789104	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10789105	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10889294	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207906	0.81[AMR][1000 genomes]
rs11207907	0.83[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11207908	0.93[ASN][1000 genomes]
rs11207909	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11207914	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022641	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12038790	0.93[ASN][1000 genomes]
rs12040256	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044746	0.81[MEX][hapmap]
rs12059368	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12071351	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12091837	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562124	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1989208	0.88[ASN][1000 genomes]
rs57176838	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60381716	0.81[AMR][1000 genomes]
rs6684324	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6687095	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs976574	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10889292	ECAT11	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
7	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:62605000-62631800	Weak transcription	Lung	lung
9	chr1:62605200-62622400	Weak transcription	Fetal Brain Female	brain
10	chr1:62605200-62624400	Weak transcription	Right Atrium	heart
11	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
12	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:62608000-62618800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:62608400-62618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:62608800-62627400	Weak transcription	Fetal Kidney	kidney
17	chr1:62609000-62620600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:62609000-62620600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:62609000-62621600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:62610800-62619600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:62610800-62621400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:62612400-62629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:62612400-62632600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:62612600-62625200	Weak transcription	GM12878-XiMat	blood
25	chr1:62613200-62619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:62613800-62621200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:62614000-62619200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:62614000-62619600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:62614000-62621200	Strong transcription	Fetal Intestine Large	intestine
31	chr1:62614000-62621400	Strong transcription	Liver	Liver
32	chr1:62614400-62628400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:62614400-62628800	Weak transcription	Ovary	ovary
34	chr1:62614600-62619400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:62614600-62620600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:62614600-62620800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:62615200-62629000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:62615200-62629400	Weak transcription	NHEK	skin
39	chr1:62615800-62619000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:62615800-62620600	Weak transcription	HepG2	liver
41	chr1:62616000-62619200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:62616000-62620000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:62616000-62625400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:62616200-62619600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:62616200-62622200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:62616200-62628200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:62616200-62629400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:62616200-62631800	Weak transcription	Right Ventricle	heart
49	chr1:62616600-62626600	Weak transcription	Left Ventricle	heart
50	chr1:62616600-62627000	Weak transcription	Fetal Stomach	stomach

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