Variant report

Variant	rs152338
Chromosome Location	chr19:19868755-19868756
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	chr19:19842402..19846588-chr19:19867933..19871933,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-1	chr19:19867916-19869355	ENSG00000228642
2	lnc-ZNF506-1	chr19:19868592-19869355	ENSG00000266904.1
3	lnc-ZNF506-1	chr19:19868610-19869355	NONHSAT063584
4	lnc-ZNF506-1	chr19:19868175-19869355	ENSG00000228642

Variant related genes	Relation type
ENSG00000105708	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs152337	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166018	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs185062	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247756	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247758	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247783	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248968	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs248970	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs248971	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1057601	chr19:19803482-19873623	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1062212	chr19:19806386-19869332	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1060122	chr19:19814678-19879575	Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv2436	chr19:19815858-19869171	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv517362	chr19:19846458-19872093	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs152338	ZNF506,LOC284440	cis	brain	BrainEAC

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19859800-19870800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19861000-19875000	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19862200-19869200	Weak transcription	Gastric	stomach
4	chr19:19862400-19869000	Weak transcription	Spleen	Spleen
5	chr19:19862800-19874000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:19862800-19886400	Weak transcription	Pancreas	Pancrea
7	chr19:19865200-19886400	Weak transcription	Right Ventricle	heart
8	chr19:19865400-19873800	Weak transcription	Ovary	ovary
9	chr19:19865600-19879000	Weak transcription	Brain Substantia Nigra	brain
10	chr19:19866200-19886000	Weak transcription	Brain Hippocampus Middle	brain
11	chr19:19867200-19875000	Weak transcription	Left Ventricle	heart
12	chr19:19867600-19870800	Weak transcription	Fetal Muscle Leg	muscle
13	chr19:19867800-19868800	Weak transcription	Adipose Nuclei	Adipose
14	chr19:19867800-19870200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:19867800-19875000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:19868000-19871200	Weak transcription	Aorta	Aorta
17	chr19:19868400-19869200	Strong transcription	Liver	Liver
18	chr19:19868400-19869200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr19:19868400-19869400	Strong transcription	Brain Cingulate Gyrus	brain
20	chr19:19868600-19869400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:19868600-19870400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links