Variant report

Variant	rs17028395
Chromosome Location	chr4:152942909-152942910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12647345	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17028387	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17028407	0.83[AMR][1000 genomes]
rs17028413	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17419220	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62318960	0.87[ASN][1000 genomes]
rs62321495	0.87[ASN][1000 genomes]
rs6844610	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7682518	0.84[ASN][1000 genomes]
rs7682524	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv461679	chr4:152935555-152992741	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv595734	chr4:152935555-152992741	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17028395	CTSO	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152937800-152944400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:152938200-152943000	Weak transcription	Fetal Brain Male	brain
3	chr4:152941600-152945400	Enhancers	Right Ventricle	heart
4	chr4:152941600-152946200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:152942000-152944600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:152942000-152946800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr4:152942200-152943400	Enhancers	Brain Substantia Nigra	brain
8	chr4:152942200-152943800	Enhancers	Brain Hippocampus Middle	brain
9	chr4:152942200-152944000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:152942200-152944400	Enhancers	Left Ventricle	heart
11	chr4:152942200-152944800	Enhancers	Brain Angular Gyrus	brain
12	chr4:152942200-152946400	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:152942400-152943000	Weak transcription	Right Atrium	heart
14	chr4:152942400-152943200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:152942400-152943800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:152942600-152943600	Enhancers	Brain Anterior Caudate	brain
17	chr4:152942600-152944200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:152942800-152943600	Enhancers	Fetal Thymus	thymus
19	chr4:152942800-152943800	Enhancers	Fetal Heart	heart

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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