Variant report

Variant	rs12978111
Chromosome Location	chr19:52890454-52890455
allele	C/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: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10415459	0.83[ASN][1000 genomes]
rs11883308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12977007	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985587	0.86[ASN][1000 genomes]
rs3170100	0.82[AMR][1000 genomes]
rs4802929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55748277	0.81[AMR][1000 genomes]
rs56151179	0.82[AMR][1000 genomes]
rs62108318	0.82[AMR][1000 genomes]
rs6509634	0.88[ASN][1000 genomes]
rs7259863	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:46 , 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	nsv580009	chr19:52887282-52890646	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv580010	chr19:52887427-52890646	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3511780	chr19:52887690-52892388	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	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
16	esv3511776	chr19:52888090-52892388	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv3394429	chr19:52888140-52892538	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3511778	chr19:52888454-52893799	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv512590	chr19:52888580-52891406	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv580011	chr19:52888620-52890646	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3318189	chr19:52888677-52891614	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3511779	chr19:52888688-52891541	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3511781	chr19:52888700-52891517	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv3318188	chr19:52888708-52891501	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
25	esv3318190	chr19:52888725-52891481	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv3318191	chr19:52888737-52891467	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv3511777	chr19:52888744-52891471	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv17108	chr19:52888750-52891129	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv3318187	chr19:52888750-52891428	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv828613	chr19:52888767-52891260	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv828614	chr19:52888767-52891450	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
32	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
33	esv3318192	chr19:52888817-52891387	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
34	esv3511782	chr19:52888817-52891387	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv580014	chr19:52888897-52890454	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv580015	chr19:52888897-52890646	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv580016	chr19:52888897-52890809	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv580018	chr19:52888950-52890454	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv580019	chr19:52888950-52890646	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
40	esv32843	chr19:52889022-52891109	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv580020	chr19:52889544-52890577	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv580021	chr19:52889544-52890646	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv580022	chr19:52889544-52890809	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
44	nsv580023	chr19:52889649-52890646	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
45	nsv580024	chr19:52890176-52890646	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
46	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12978111	ZNF880	cis	Adipose Subcutaneous	GTEx
rs12978111	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs12978111	ZNF880	cis	Artery Tibial	GTEx
rs12978111	ZNF880	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52890600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:52876200-52890600	ZNF genes & repeats	Fetal Lung	lung
3	chr19:52876200-52890800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52876200-52890800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:52876200-52890800	ZNF genes & repeats	Liver	Liver
6	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:52876400-52890600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr19:52876400-52891000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr19:52879000-52890600	ZNF genes & repeats	Colon Smooth Muscle	Colon
17	chr19:52880200-52890600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
19	chr19:52882000-52890600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr19:52885800-52890600	ZNF genes & repeats	Osteobl	bone
21	chr19:52885800-52890800	ZNF genes & repeats	Brain Hippocampus Middle	brain
22	chr19:52886000-52893400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:52886600-52890600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
24	chr19:52886600-52890600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
25	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:52888600-52891200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:52888600-52891400	Weak transcription	Thymus	Thymus
28	chr19:52888600-52892800	Weak transcription	Right Ventricle	heart
29	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:52888800-52891200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:52888800-52891800	Weak transcription	NH-A	brain
32	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
33	chr19:52889000-52891200	Weak transcription	Placenta	Placenta
34	chr19:52889000-52891400	Weak transcription	HSMMtube	muscle
35	chr19:52889000-52891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:52889000-52891800	Weak transcription	Brain Substantia Nigra	brain
37	chr19:52889000-52891800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:52889000-52892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:52889000-52892800	Weak transcription	HSMM	muscle
40	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
42	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
43	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:52889400-52892600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:52889600-52891800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:52889600-52891800	Weak transcription	Fetal Kidney	kidney
47	chr19:52889800-52891400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:52889800-52891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:52889800-52891600	Weak transcription	Left Ventricle	heart
50	chr19:52889800-52892000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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