Variant report

Variant	rs12462953
Chromosome Location	chr19:52840918-52840919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
2	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:
3	chr19:52641710..52644473-chr19:52838292..52841252,2	MCF-7	breast:
4	chr19:52828291..52831274-chr19:52840252..52843029,2	K562	blood:
5	chr19:52835793..52838110-chr19:52840085..52841943,2	K562	blood:
6	chr19:52839189..52842101-chr19:52900021..52902093,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000269834	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10404965	0.93[ASN][1000 genomes]
rs10405321	0.93[ASN][1000 genomes]
rs10407594	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408636	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10411053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415728	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10419765	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10425327	0.84[ASN][1000 genomes]
rs11084148	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540745	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs167707	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs167708	0.82[ASN][1000 genomes]
rs170414	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1810006	0.90[ASN][1000 genomes]
rs2115075	0.83[ASN][1000 genomes]
rs2115076	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321902	0.82[ASN][1000 genomes]
rs321919	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs321921	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs321922	0.89[ASN][1000 genomes]
rs321923	0.91[ASN][1000 genomes]
rs321924	0.87[ASN][1000 genomes]
rs321925	0.89[ASN][1000 genomes]
rs321926	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs321935	0.84[JPT][hapmap]
rs4801912	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7249784	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7256570	0.91[ASN][1000 genomes]
rs7258711	0.81[ASN][1000 genomes]
rs7260178	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102373	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109096	0.91[CEU][hapmap]
rs8112051	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs8112337	0.87[CEU][hapmap]
rs890842	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs890843	0.87[EUR][1000 genomes];1.00[ASN][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	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12462953	ZNF480	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
2	chr19:52838800-52841200	Active TSS	Fetal Kidney	kidney
3	chr19:52839200-52841000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52839200-52842200	ZNF genes & repeats	Lung	lung
5	chr19:52840200-52841000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:52840200-52841000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr19:52840200-52841200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:52840400-52841000	Flanking Active TSS	Fetal Brain Female	brain
9	chr19:52840400-52841000	Enhancers	Fetal Heart	heart
10	chr19:52840400-52841000	Flanking Active TSS	Dnd41	blood
11	chr19:52840400-52841200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:52840400-52841800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:52840400-52842000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:52840400-52848200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:52840600-52841000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:52840600-52841000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:52840600-52841000	Enhancers	Primary T cells from cord blood	blood
20	chr19:52840600-52841000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:52840600-52841000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:52840600-52841000	Weak transcription	Brain Angular Gyrus	brain
23	chr19:52840600-52841000	Enhancers	Brain Hippocampus Middle	brain
24	chr19:52840600-52841000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:52840600-52841000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:52840600-52841000	Enhancers	Fetal Lung	lung
27	chr19:52840600-52841000	Enhancers	Fetal Stomach	stomach
28	chr19:52840600-52841200	Weak transcription	Primary B cells from cord blood	blood
29	chr19:52840600-52841200	Weak transcription	HUVEC	blood vessel
30	chr19:52840600-52841200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr19:52840600-52841400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:52840600-52841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:52840600-52842000	Weak transcription	Spleen	Spleen
34	chr19:52840600-52842200	Weak transcription	NH-A	brain
35	chr19:52840600-52842400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:52840600-52842600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:52840600-52847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:52840600-52847000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:52840600-52847000	Weak transcription	Brain Anterior Caudate	brain
40	chr19:52840600-52847000	Weak transcription	Brain Substantia Nigra	brain
41	chr19:52840600-52847600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:52840600-52848400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:52840600-52850400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:52840600-52850800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:52840600-52850800	Weak transcription	Ovary	ovary
46	chr19:52840600-52851000	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:52840600-52851000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:52840600-52851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:52840600-52851200	Weak transcription	Placenta	Placenta
50	chr19:52840600-52851600	Weak transcription	Left Ventricle	heart

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