Variant report

Variant	rs958728
Chromosome Location	chr19:39995395-39995396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000105193	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10410648	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425652	0.85[MEX][hapmap]
rs4803254	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56194215	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9967597	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs958728	SFRS16	cis	cerebellum	SCAN
rs958728	PRX	cis	parietal	SCAN
rs958728	BSPH1	cis	parietal	SCAN
rs958728	ZNF296	cis	parietal	SCAN
rs958728	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs958728	NUMBL	cis	parietal	SCAN
rs958728	RPS16	cis	lymphoblastoid	seeQTL
rs958728	CYP2F1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39989400-39997600	Weak transcription	Right Atrium	heart
2	chr19:39990200-39997600	Weak transcription	Gastric	stomach
3	chr19:39991400-39996400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:39994000-39996400	Strong transcription	Brain Germinal Matrix	brain
5	chr19:39994000-39997200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:39994000-39997400	Weak transcription	Fetal Brain Male	brain
7	chr19:39994000-39997600	Weak transcription	Pancreas	Pancrea
8	chr19:39994200-39995800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39994200-39995800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:39994200-39997200	Weak transcription	K562	blood
11	chr19:39994400-39996000	Strong transcription	Fetal Brain Female	brain
12	chr19:39995200-39997200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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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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