Variant report

Variant	rs16881847
Chromosome Location	chr5:53215330-53215331
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10040674	0.90[ASN][1000 genomes]
rs13170364	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs13187145	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs16881895	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17251005	0.86[JPT][hapmap]
rs1838724	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3816974	0.81[ASN][1000 genomes]
rs56016819	0.87[ASN][1000 genomes]
rs58614496	0.94[ASN][1000 genomes]
rs60633530	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs66505436	0.87[ASN][1000 genomes]
rs68101674	0.87[ASN][1000 genomes]
rs713209	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7726524	0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv598175	chr5:53213945-53230760	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv880272	chr5:53213945-53277266	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16881847	ISL1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:53187600-53232800	Weak transcription	Primary T cells from cord blood	blood
3	chr5:53189800-53216600	Weak transcription	Left Ventricle	heart
4	chr5:53200800-53251600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:53206800-53236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:53213400-53215400	Enhancers	Fetal Brain Male	brain
7	chr5:53213400-53219000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:53213600-53219800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:53213600-53220200	Weak transcription	HSMM	muscle
10	chr5:53213800-53218800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:53213800-53219800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:53213800-53219800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:53213800-53220200	Weak transcription	Fetal Stomach	stomach
14	chr5:53213800-53225600	Weak transcription	Fetal Intestine Large	intestine
15	chr5:53213800-53235200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:53214000-53238600	Weak transcription	K562	blood
17	chr5:53215000-53215400	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr5:53215000-53215600	Enhancers	Fetal Brain Female	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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