Variant report

Variant	rs324122
Chromosome Location	chr19:52893957-52893958
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	chr19:52892095-52894826	ENSG00000269834.1

Variant related genes	Relation type
ENSG00000269834	Chromatin interaction
ENSG00000167555	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs162117	0.82[EUR][1000 genomes]
rs162126	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162127	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs182751	0.87[EUR][1000 genomes]
rs2657916	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs324121	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs324124	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs324125	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58617441	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707311	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73581131	0.82[EUR][1000 genomes]
rs810592	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
14	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs324122	LOC400713,ZNF880	cis	inferior olivary nucleus	BrainEAC
rs324122	LOC400713,ZNF880	cis	intralobular white matter	BrainEAC
rs324122	LOC400713,ZNF880	cis	frontal cortex	BrainEAC
rs324122	LOC400713,ZNF880	cis	cerebellar cortex	BrainEAC
rs324122	LOC400713,ZNF880	cis	occipital cortex	BrainEAC
rs324122	LOC400713,ZNF880	cis	temporal cortex	BrainEAC
rs324122	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs324122	LOC400713,ZNF880	cis	brain	BrainEAC
rs324122	LOC400713,ZNF880	cis	thalamus	BrainEAC

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
9	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
11	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
12	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:52889800-52898600	Weak transcription	Fetal Heart	heart
14	chr19:52890600-52897600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:52890600-52898600	Weak transcription	NHDF-Ad	bronchial
16	chr19:52890800-52897600	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:52891200-52894000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
18	chr19:52891200-52896600	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr19:52891400-52895200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr19:52891400-52895800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:52891400-52896800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:52891600-52894000	ZNF genes & repeats	Left Ventricle	heart
24	chr19:52891600-52894600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:52891600-52899800	ZNF genes & repeats	Fetal Brain Female	brain
26	chr19:52891800-52894000	ZNF genes & repeats	Liver	Liver
27	chr19:52891800-52895400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr19:52891800-52896600	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr19:52892000-52894800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:52892200-52898200	Weak transcription	HSMMtube	muscle
31	chr19:52892400-52894600	ZNF genes & repeats	Lung	lung
32	chr19:52892600-52894000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:52892600-52894000	ZNF genes & repeats	Aorta	Aorta
34	chr19:52892600-52894000	ZNF genes & repeats	Pancreas	Pancrea
35	chr19:52892600-52895400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:52893000-52898200	Weak transcription	Brain Substantia Nigra	brain
37	chr19:52893400-52894600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:52893400-52900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:52893600-52897600	Weak transcription	Dnd41	blood
40	chr19:52893600-52898200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:52893600-52898200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:52893800-52896400	Weak transcription	Fetal Lung	lung
43	chr19:52893800-52896800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:52893800-52897400	Weak transcription	Ovary	ovary
45	chr19:52893800-52897600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:52893800-52898000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:52893800-52899600	Weak transcription	Right Ventricle	heart

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