Variant report

Variant	rs1895373
Chromosome Location	chr19:51109793-51109794
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10409194	0.82[MEX][hapmap]
rs10426057	0.82[EUR][1000 genomes]
rs16986142	0.82[EUR][1000 genomes]
rs1895374	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6509490	0.83[ASN][1000 genomes]
rs7253426	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7253669	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258762	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1062281	chr19:51053340-51230844	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1062548	chr19:51081358-51230844	Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1065222	chr19:51084705-51136844	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3318822	chr19:51105140-51110238	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv512587	chr19:51105760-51109851	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3491575	chr19:51105940-51110738	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv16242	chr19:51106142-51111826	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3491577	chr19:51106690-51109988	Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3374132	chr19:51108440-51113138	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv828581	chr19:51109572-51124716	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv961234	chr19:51109635-51126366	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1895373	SYT3	cis	Esophagus Mucosa	GTEx
rs1895373	MYADM	cis	parietal	SCAN
rs1895373	TTYH1	cis	parietal	SCAN
rs1895373	ZNF324	cis	cerebellum	SCAN
rs1895373	ZNF772	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51107800-51109800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:51109000-51109800	Active TSS	Brain Substantia Nigra	brain
3	chr19:51109000-51110800	Active TSS	Brain Anterior Caudate	brain
4	chr19:51109000-51110800	Enhancers	Brain Hippocampus Middle	brain
5	chr19:51109200-51109800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:51109400-51109800	Enhancers	Brain Cingulate Gyrus	brain
7	chr19:51109400-51110200	Enhancers	K562	blood
8	chr19:51109400-51110800	Weak transcription	Brain Angular Gyrus	brain

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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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