Variant report

Variant	rs170414
Chromosome Location	chr19:52839813-52839814
allele	A/G
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	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
3	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:
4	chr19:52641710..52644473-chr19:52838292..52841252,2	MCF-7	breast:
5	chr19:52839189..52842101-chr19:52900021..52902093,2	MCF-7	breast:

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

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10404965	0.97[ASN][1000 genomes]
rs10405321	0.97[ASN][1000 genomes]
rs10407594	0.94[ASN][1000 genomes]
rs10408636	0.94[ASN][1000 genomes]
rs10411053	0.97[ASN][1000 genomes]
rs10415728	0.94[ASN][1000 genomes]
rs10419765	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11084148	0.97[ASN][1000 genomes]
rs12462904	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12462953	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]
rs1540745	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167707	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs167708	0.90[ASN][1000 genomes]
rs1810006	0.97[ASN][1000 genomes]
rs2115075	0.87[ASN][1000 genomes]
rs2115076	0.96[ASN][1000 genomes]
rs2657933	0.84[ASN][1000 genomes]
rs321902	0.90[ASN][1000 genomes]
rs321919	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321922	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321923	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321924	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321925	0.98[ASN][1000 genomes]
rs321926	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs321928	0.88[ASN][1000 genomes]
rs321932	0.88[ASN][1000 genomes]
rs321934	0.86[ASN][1000 genomes]
rs321935	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4801912	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7247178	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7249338	0.83[ASN][1000 genomes]
rs7249784	0.94[ASN][1000 genomes]
rs7256570	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258711	0.83[ASN][1000 genomes]
rs7260178	0.90[ASN][1000 genomes]
rs8102373	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8109096	0.87[CEU][hapmap]
rs8112051	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs8112337	0.83[CEU][hapmap]
rs890842	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs890843	0.91[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
rs170414	ZNF480	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
2	chr19:52838600-52840000	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr19:52838600-52840200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr19:52838600-52840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr19:52838600-52840600	ZNF genes & repeats	Pancreas	Pancrea
6	chr19:52838600-52840600	ZNF genes & repeats	Spleen	Spleen
7	chr19:52838600-52840800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:52838600-52840800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:52838600-52840800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:52838800-52840000	Active TSS	Brain Angular Gyrus	brain
11	chr19:52838800-52840000	Active TSS	Brain Anterior Caudate	brain
12	chr19:52838800-52840000	Active TSS	Brain Hippocampus Middle	brain
13	chr19:52838800-52840000	Active TSS	Rectal Smooth Muscle	rectum
14	chr19:52838800-52840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:52838800-52840200	Active TSS	Primary T cells from cord blood	blood
16	chr19:52838800-52840200	Active TSS	Brain Cingulate Gyrus	brain
17	chr19:52838800-52840200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:52838800-52840400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:52838800-52840400	Active TSS	Fetal Brain Female	brain
20	chr19:52838800-52840400	Active TSS	Psoas Muscle	Psoas
21	chr19:52838800-52840400	ZNF genes & repeats	GM12878-XiMat	blood
22	chr19:52838800-52840800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:52838800-52840800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr19:52838800-52841200	Active TSS	Fetal Kidney	kidney
25	chr19:52839000-52840000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:52839000-52840000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr19:52839000-52840200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:52839000-52840200	Active TSS	Brain Substantia Nigra	brain
29	chr19:52839000-52840200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr19:52839000-52840200	Active TSS	Fetal Stomach	stomach
31	chr19:52839000-52840200	Active TSS	Left Ventricle	heart
32	chr19:52839000-52840200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr19:52839000-52840400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:52839000-52840400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:52839000-52840400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:52839000-52840400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:52839000-52840400	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr19:52839000-52840400	Active TSS	Colonic Mucosa	Colon
39	chr19:52839000-52840400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr19:52839000-52840400	Active TSS	Fetal Lung	lung
41	chr19:52839000-52840400	Active TSS	Ovary	ovary
42	chr19:52839000-52840400	Active TSS	Right Atrium	heart
43	chr19:52839000-52840400	Active TSS	Right Ventricle	heart
44	chr19:52839000-52840600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:52839000-52840600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr19:52839000-52840800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr19:52839000-52840800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr19:52839000-52840800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr19:52839000-52840800	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr19:52839000-52840800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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