Variant report

Variant	rs1593516
Chromosome Location	chr1:93899133-93899134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11164939	0.89[ASN][1000 genomes]
rs11164941	0.88[ASN][1000 genomes]
rs12034656	0.85[ASN][1000 genomes]
rs17109958	0.92[ASN][1000 genomes]
rs2433279	0.92[ASN][1000 genomes]
rs61780647	0.93[ASN][1000 genomes]
rs61784068	0.86[ASN][1000 genomes]
rs7543847	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3375834	chr1:93872980-93904647	ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1593516	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1593516	RP4-717I23.3	cis	Artery Tibial	GTEx
rs1593516	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs1593516	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93893600-93899200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93893600-93899200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:93893600-93899400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:93898000-93900000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:93898600-93899400	Enhancers	Adipose Nuclei	Adipose
6	chr1:93898800-93899600	Enhancers	Liver	Liver
7	chr1:93899000-93899200	Enhancers	HepG2	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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