Variant report

Variant	rs2560885
Chromosome Location	chr19:52861522-52861523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52861409..52864151-chr19:52865571..52868442,2	MCF-7	breast:
2	chr19:52839457..52840970-chr19:52859823..52861892,2	MCF-7	breast:
3	chr19:52861080..52862902-chr19:52863243..52865852,2	K562	blood:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10401360	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10419807	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1120184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666043	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11666131	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11667184	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670904	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11881435	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2115102	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247987	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2263899	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2263901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2434418	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2434460	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560883	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560990	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560991	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657937	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657938	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657940	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2903978	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2903979	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35017258	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59043312	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62108276	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62108308	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62108309	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62108312	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2560885	ZNF480	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
3	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
6	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
9	chr19:52856600-52864200	ZNF genes & repeats	Liver	Liver
10	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
11	chr19:52857600-52865200	Strong transcription	Brain Hippocampus Middle	brain
12	chr19:52858000-52862000	Strong transcription	Fetal Kidney	kidney
13	chr19:52858200-52861600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:52858200-52863200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:52858200-52863200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:52858200-52863600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:52858400-52866800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:52858800-52871800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:52859200-52862600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:52859400-52863200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:52859600-52862600	Weak transcription	Brain Substantia Nigra	brain
22	chr19:52859600-52865200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:52859600-52866000	Strong transcription	Dnd41	blood
24	chr19:52859600-52868800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:52859800-52865000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:52859800-52866800	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:52859800-52868200	Weak transcription	Right Ventricle	heart
28	chr19:52860200-52861800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:52860200-52862400	Weak transcription	Brain Angular Gyrus	brain
30	chr19:52860200-52862600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:52860200-52862800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:52860200-52862800	Weak transcription	Fetal Brain Male	brain
33	chr19:52860200-52862800	Weak transcription	Gastric	stomach
34	chr19:52860200-52863600	ZNF genes & repeats	Fetal Intestine Large	intestine
35	chr19:52860400-52861600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:52860400-52861600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
37	chr19:52860400-52862000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:52860400-52862000	Weak transcription	HSMMtube	muscle
39	chr19:52860400-52862200	Weak transcription	Adipose Nuclei	Adipose
40	chr19:52860400-52862600	Weak transcription	Left Ventricle	heart
41	chr19:52860400-52864400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:52860600-52861600	ZNF genes & repeats	Fetal Stomach	stomach
43	chr19:52860600-52861800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:52860600-52862000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:52860600-52862000	Weak transcription	Psoas Muscle	Psoas
46	chr19:52860600-52862800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:52860600-52864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:52860600-52865200	Weak transcription	Placenta	Placenta
49	chr19:52860800-52861800	Weak transcription	Brain Anterior Caudate	brain
50	chr19:52861000-52861600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

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