Variant report

Variant	rs324121
Chromosome Location	chr19:52894445-52894446
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	chr19:52893005..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: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs162117	0.90[EUR][1000 genomes]
rs162126	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162127	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs182751	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2657916	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs324120	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs324122	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs324124	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs324125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58617441	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs707311	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73581131	0.89[EUR][1000 genomes]
rs810592	0.81[AMR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs324121	LOC400713	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
5	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
8	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:52889800-52898600	Weak transcription	Fetal Heart	heart
10	chr19:52890600-52897600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:52890600-52898600	Weak transcription	NHDF-Ad	bronchial
12	chr19:52890800-52897600	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:52891200-52896600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:52891400-52895200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:52891400-52895800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:52891400-52896800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:52891600-52894600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:52891600-52899800	ZNF genes & repeats	Fetal Brain Female	brain
20	chr19:52891800-52895400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
21	chr19:52891800-52896600	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr19:52892000-52894800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:52892200-52898200	Weak transcription	HSMMtube	muscle
24	chr19:52892400-52894600	ZNF genes & repeats	Lung	lung
25	chr19:52892600-52895400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:52893000-52898200	Weak transcription	Brain Substantia Nigra	brain
27	chr19:52893400-52894600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:52893400-52900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:52893600-52897600	Weak transcription	Dnd41	blood
30	chr19:52893600-52898200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:52893600-52898200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:52893800-52896400	Weak transcription	Fetal Lung	lung
33	chr19:52893800-52896800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:52893800-52897400	Weak transcription	Ovary	ovary
35	chr19:52893800-52897600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:52893800-52898000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr19:52893800-52899600	Weak transcription	Right Ventricle	heart
38	chr19:52894000-52895000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:52894000-52897600	Weak transcription	Pancreas	Pancrea
40	chr19:52894000-52898200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:52894000-52900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:52894400-52894600	ZNF genes & repeats	Aorta	Aorta
43	chr19:52894400-52894600	ZNF genes & repeats	Left Ventricle	heart

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