Variant report

Variant	rs11659388
Chromosome Location	chr18:44278843-44278844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1038005	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075892	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11659721	0.88[AFR][1000 genomes]
rs11662364	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11663996	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16939988	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17778494	0.81[AMR][1000 genomes]
rs17778939	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs41471844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs4890336	0.84[MEX][hapmap]
rs4890337	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4890683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890685	1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514285	0.86[EUR][1000 genomes]
rs56154750	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56350359	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650329	0.96[CEU][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72917404	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9807683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428355	chr18:44160181-44406285	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3397234	chr18:44276654-44279552	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11659388	ST8SIA5	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44253000-44291400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:44258200-44280000	Weak transcription	HSMMtube	muscle
3	chr18:44260800-44286600	Weak transcription	Brain Germinal Matrix	brain
4	chr18:44273200-44288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:44276600-44286600	Weak transcription	Left Ventricle	heart
6	chr18:44277000-44282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr18:44277000-44282200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr18:44277000-44282400	Weak transcription	Psoas Muscle	Psoas
9	chr18:44278400-44280600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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