Variant report

Variant	rs854796
Chromosome Location	chr17:18070761-18070762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12051649	0.93[ASN][1000 genomes]
rs2075657	0.99[ASN][1000 genomes]
rs2473656	0.82[ASN][1000 genomes]
rs2605133	0.81[ASN][1000 genomes]
rs4925144	0.99[ASN][1000 genomes]
rs59588957	0.99[ASN][1000 genomes]
rs712271	0.81[ASN][1000 genomes]
rs712274	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72831919	0.92[ASN][1000 genomes]
rs854773	0.81[ASN][1000 genomes]
rs854774	0.81[ASN][1000 genomes]
rs854777	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs854800	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854802	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854803	0.99[ASN][1000 genomes]
rs9899249	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9903403	0.93[ASN][1000 genomes]
rs9903591	0.93[ASN][1000 genomes]
rs9913262	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs854796	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854796	LGALS9C	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
2	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
3	chr17:18064800-18085400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:18067800-18071000	Weak transcription	Fetal Intestine Large	intestine
5	chr17:18067800-18071000	Weak transcription	Fetal Intestine Small	intestine
6	chr17:18069800-18070800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:18070000-18075200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr17:18070200-18071000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:18070400-18071200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:18070400-18072800	Weak transcription	Liver	Liver
11	chr17:18070400-18075000	Weak transcription	Ovary	ovary
12	chr17:18070600-18071200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:18070600-18071200	ZNF genes & repeats	Spleen	Spleen

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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