Variant report

Variant	rs10417830
Chromosome Location	chr19:35958677-35958678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10408094	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419824	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17638216	1.00[CHD][hapmap]
rs28439691	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60038395	0.93[EUR][1000 genomes]
rs7245569	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7248666	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7976	1.00[CHD][hapmap]
rs9916947	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9973222	1.00[CHD][hapmap];0.92[MEX][hapmap]

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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
5	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1057692	chr19:35949892-35984103	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv543994	chr19:35949892-35984103	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10417830	SYCN	cis	parietal	SCAN
rs10417830	PSG1	cis	parietal	SCAN
rs10417830	ZFP30	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35941600-35970200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:35955000-35958800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr19:35955000-35959400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr19:35955200-35958800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:35955200-35959000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:35955400-35959600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:35955400-35959600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:35955800-35959200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:35956000-35959200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:35956000-35959400	Weak transcription	Primary B cells from cord blood	blood
11	chr19:35957400-35961800	Enhancers	HepG2	liver
12	chr19:35957600-35959800	Enhancers	Adipose Nuclei	Adipose
13	chr19:35957800-35961400	Enhancers	GM12878-XiMat	blood
14	chr19:35958200-35958800	Enhancers	Placenta	Placenta
15	chr19:35958400-35959000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:35958600-35959600	Weak transcription	Liver	Liver

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

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