Variant report

Variant	rs1343520
Chromosome Location	chr1:75885982-75885983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1036950	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs10747387	0.88[CHB][hapmap]
rs10874264	0.83[ASN][1000 genomes]
rs1107148	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1116878	0.88[CHB][hapmap]
rs12402118	0.87[CHB][hapmap]
rs1249784	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1249786	0.88[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs1249794	0.81[CHB][hapmap]
rs1343519	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1571983	0.81[CHB][hapmap]
rs1858627	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs1858628	0.81[CHB][hapmap]
rs1891902	0.87[CHB][hapmap]
rs1936358	0.81[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2347214	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[MKK][hapmap];0.80[ASN][1000 genomes]
rs2587042	0.88[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2972005	0.80[CHB][hapmap]
rs6675276	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3441748	chr1:75866980-75890018	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1011915	chr1:75879330-75934553	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1343520	TYW3	cis	parietal	SCAN
rs1343520	SLC44A5	cis	normal skin	skin_eQTL
rs1343520	AK5	cis	cerebellum	SCAN
rs1343520	SLC44A5	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75883800-75889000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:75885600-75886000	Enhancers	K562	blood

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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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