Variant report

Variant	rs1535388
Chromosome Location	chr10:116165248-116165249
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10885558	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10885564	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11196727	0.84[AMR][1000 genomes]
rs1575232	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2151891	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4751864	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4752638	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4752729	0.86[EUR][1000 genomes]
rs6585276	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7084061	0.80[AMR][1000 genomes]
rs7088109	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7099520	0.84[AMR][1000 genomes]
rs7906164	0.80[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7910402	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7917021	0.86[EUR][1000 genomes]
rs941856	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv3340687	chr10:116162987-116165535	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1535388	AFAP1L2	cis	cerebellum	SCAN
rs1535388	PNLIPRP3	cis	cerebellum	SCAN
rs1535388	LOC143188	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116162600-116165400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr10:116162600-116165600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr10:116163200-116165400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr10:116164600-116165400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:116164600-116165400	Flanking Active TSS	HMEC	breast
6	chr10:116164800-116165400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:116164800-116165400	Flanking Active TSS	A549	lung
8	chr10:116164800-116165400	Flanking Active TSS	NHEK	skin
9	chr10:116165000-116165400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:116165000-116165400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr10:116165000-116165400	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr10:116165000-116165600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:116165000-116172000	Weak transcription	Esophagus	oesophagus
14	chr10:116165000-116172600	Weak transcription	Pancreas	Pancrea
15	chr10:116165200-116165400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr10:116165200-116165600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr10:116165200-116166000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:116165200-116167600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:116165200-116167600	Weak transcription	Spleen	Spleen

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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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