Variant report

Variant	rs17780037
Chromosome Location	chr19:52891464-52891465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52875265..52876916-chr19:52889763..52892567,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17780009	0.86[ASN][1000 genomes]
rs965222	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription 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	11 gene(s)	inside rSNPs	diseases
11	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	esv3511780	chr19:52887690-52892388	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv511613	chr19:52888071-52895166	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv3511776	chr19:52888090-52892388	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv3394429	chr19:52888140-52892538	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv3511778	chr19:52888454-52893799	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv3318189	chr19:52888677-52891614	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3511779	chr19:52888688-52891541	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3511781	chr19:52888700-52891517	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv3318188	chr19:52888708-52891501	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3318190	chr19:52888725-52891481	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3318191	chr19:52888737-52891467	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3511777	chr19:52888744-52891471	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv580025	chr19:52890176-52895885	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17780037	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs17780037	ZNF880	cis	Artery Tibial	GTEx
rs17780037	ZNF880	cis	Esophagus Muscularis	GTEx
rs17780037	ZNF880	cis	Adipose Subcutaneous	GTEx
rs17780037	ZNF880	cis	Heart Left Ventricle	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
10	chr19:52886000-52893400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:52888600-52892800	Weak transcription	Right Ventricle	heart
13	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:52888800-52891800	Weak transcription	NH-A	brain
15	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
16	chr19:52889000-52891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52889000-52891800	Weak transcription	Brain Substantia Nigra	brain
18	chr19:52889000-52891800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:52889000-52892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:52889000-52892800	Weak transcription	HSMM	muscle
21	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
23	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
24	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:52889400-52892600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:52889600-52891800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:52889600-52891800	Weak transcription	Fetal Kidney	kidney
28	chr19:52889800-52891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:52889800-52891600	Weak transcription	Left Ventricle	heart
30	chr19:52889800-52892000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:52889800-52892600	Weak transcription	Pancreas	Pancrea
32	chr19:52889800-52898600	Weak transcription	Fetal Heart	heart
33	chr19:52890000-52892000	Strong transcription	Ovary	ovary
34	chr19:52890600-52891600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:52890600-52891800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:52890600-52891800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:52890600-52891800	Weak transcription	Dnd41	blood
38	chr19:52890600-52892000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:52890600-52892400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:52890600-52897600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:52890600-52898600	Weak transcription	NHDF-Ad	bronchial
42	chr19:52890800-52891800	Weak transcription	Liver	Liver
43	chr19:52890800-52897600	Weak transcription	Brain Hippocampus Middle	brain
44	chr19:52891200-52893200	ZNF genes & repeats	Placenta	Placenta
45	chr19:52891200-52894000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr19:52891200-52896600	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr19:52891400-52892200	Strong transcription	HSMMtube	muscle
49	chr19:52891400-52893200	ZNF genes & repeats	Thymus	Thymus
50	chr19:52891400-52895200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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