Variant report

Variant	rs66539779
Chromosome Location	chr10:43942394-43942395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr10:43942297-43942567	GM12878	blood:	n/a	n/a
2	SETDB1	chr10:43942108-43942496	U2OS	brain:	n/a	n/a
3	KAP1	chr10:43942127-43942525	HEK293	kidney:	n/a	n/a
4	CTCF	chr10:43942374-43942472	GM13976	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43941921..43943568-chr10:43945828..43947483,2	MCF-7	breast:
2	chr10:43941606..43943262-chr10:43948647..43951071,2	K562	blood:
3	chr10:43939246..43942675-chr10:43946277..43949309,3	MCF-7	breast:

Variant related genes	Relation type
ZNF487	TF binding region
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10444669	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10483452	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1091349	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11620737	0.86[ASN][1000 genomes]
rs11620951	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11623118	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11623882	0.83[ASN][1000 genomes]
rs11624462	0.86[ASN][1000 genomes]
rs11625046	0.87[ASN][1000 genomes]
rs11625507	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11625810	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11625942	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626113	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11627958	0.83[ASN][1000 genomes]
rs11628446	0.90[ASN][1000 genomes]
rs12881415	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12882986	0.87[ASN][1000 genomes]
rs12888766	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1627716	0.83[ASN][1000 genomes]
rs1712354	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1738799	0.87[ASN][1000 genomes]
rs34116113	0.83[ASN][1000 genomes]
rs34319196	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34658054	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34844770	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35361707	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468265	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35861323	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432181	0.83[ASN][1000 genomes]
rs55805245	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55815172	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56240056	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56380926	0.86[ASN][1000 genomes]
rs61988266	0.86[ASN][1000 genomes]
rs61989479	0.87[ASN][1000 genomes]
rs61989495	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61989543	0.83[ASN][1000 genomes]
rs61989544	0.86[ASN][1000 genomes]
rs61989545	0.90[ASN][1000 genomes]
rs61989546	0.93[ASN][1000 genomes]
rs61989547	0.93[ASN][1000 genomes]
rs71421926	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7145645	0.81[ASN][1000 genomes]
rs799455	0.87[ASN][1000 genomes]
rs799456	0.87[ASN][1000 genomes]
rs799465	0.84[ASN][1000 genomes]
rs799466	0.87[ASN][1000 genomes]
rs799470	0.83[ASN][1000 genomes]
rs799471	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs799472	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs799475	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs799481	0.87[ASN][1000 genomes]
rs799482	0.87[ASN][1000 genomes]
rs799485	0.83[ASN][1000 genomes]
rs799489	0.87[ASN][1000 genomes]
rs799490	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs799493	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs799494	0.87[ASN][1000 genomes]
rs799496	0.87[ASN][1000 genomes]
rs876144	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
7	esv3448813	chr10:43919995-43950867	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1043746	chr10:43940898-43977155	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43933000-43947200	Weak transcription	Spleen	Spleen
2	chr10:43933000-43949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:43933000-43950200	Weak transcription	Lung	lung
4	chr10:43933200-43947600	Weak transcription	Brain Anterior Caudate	brain
5	chr10:43933200-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:43933200-43950000	Weak transcription	Brain Substantia Nigra	brain
7	chr10:43933200-43950200	Weak transcription	Brain Angular Gyrus	brain
8	chr10:43933200-43950200	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:43933200-43950200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:43933200-43950200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr10:43933400-43948000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:43933600-43947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:43933600-43947400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:43933600-43948200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:43933600-43948200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:43933600-43949800	Weak transcription	Adipose Nuclei	Adipose
17	chr10:43933800-43946600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:43934200-43949200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:43936400-43943800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:43936400-43950000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr10:43936600-43946000	Weak transcription	Primary B cells from cord blood	blood
22	chr10:43936800-43944200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr10:43938600-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:43940000-43943800	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr10:43940000-43946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:43940200-43950200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:43940400-43943800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:43940400-43950200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:43940400-43950200	Weak transcription	Colonic Mucosa	Colon
30	chr10:43940800-43944800	Weak transcription	Primary T cells from cord blood	blood
31	chr10:43940800-43947200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr10:43940800-43949600	Weak transcription	Hela-S3	cervix
33	chr10:43940800-43950600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:43941000-43942400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:43941200-43947200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:43941800-43943200	ZNF genes & repeats	Fetal Stomach	stomach
37	chr10:43942200-43943000	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr10:43942200-43946000	Weak transcription	Thymus	Thymus

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