Variant report

Variant	rs2657916
Chromosome Location	chr19:52893539-52893540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52893005..52896642-chr19:52900305..52903556,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-1	chr19:52892095-52896456	ENSG00000246015
2	lnc-ZNF83-1	chr19:52892095-52893679	ENSG00000246015
3	lnc-ZNF83-1	chr19:52892095-52894826	ENSG00000269834.1

Variant related genes	Relation type
ENSG00000167555	Chromatin interaction
ENSG00000269834	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs162117	0.83[EUR][1000 genomes]
rs162126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162127	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182751	0.88[EUR][1000 genomes]
rs324121	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs324122	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs324124	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs324125	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58617441	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs707311	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73581131	0.82[EUR][1000 genomes]
rs810592	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
13	esv3511778	chr19:52888454-52893799	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	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
15	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2657916	LOC400713	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
9	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
12	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
14	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
15	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:52889800-52898600	Weak transcription	Fetal Heart	heart
17	chr19:52890600-52897600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr19:52890600-52898600	Weak transcription	NHDF-Ad	bronchial
19	chr19:52890800-52897600	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:52891200-52894000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
21	chr19:52891200-52896600	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr19:52891400-52895200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr19:52891400-52895800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:52891400-52896800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:52891600-52893800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:52891600-52893800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:52891600-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:52891600-52893800	ZNF genes & repeats	Fetal Lung	lung
30	chr19:52891600-52893800	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr19:52891600-52894000	ZNF genes & repeats	Left Ventricle	heart
32	chr19:52891600-52894600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:52891600-52899800	ZNF genes & repeats	Fetal Brain Female	brain
34	chr19:52891800-52893600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
35	chr19:52891800-52893800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:52891800-52893800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:52891800-52893800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr19:52891800-52894000	ZNF genes & repeats	Liver	Liver
39	chr19:52891800-52895400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr19:52891800-52896600	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr19:52892000-52893800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
42	chr19:52892000-52893800	ZNF genes & repeats	Ovary	ovary
43	chr19:52892000-52893800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:52892000-52894800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:52892200-52893800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:52892200-52898200	Weak transcription	HSMMtube	muscle
47	chr19:52892400-52893600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:52892400-52894600	ZNF genes & repeats	Lung	lung
49	chr19:52892600-52893800	ZNF genes & repeats	Colonic Mucosa	Colon
50	chr19:52892600-52894000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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