Variant report

Variant	rs11742341
Chromosome Location	chr5:5239921-5239922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11742370	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13154610	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs16875128	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs17712889	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17713759	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17713940	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2019251	0.82[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2059798	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081850	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2913628	0.87[CEU][hapmap]
rs2913630	0.83[CEU][hapmap]
rs2913631	0.87[CEU][hapmap]
rs2913632	0.87[CEU][hapmap]
rs2964429	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34880199	0.85[EUR][1000 genomes]
rs35009703	0.88[EUR][1000 genomes]
rs35061588	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55706045	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55819445	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56307540	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72724162	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72724173	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs919244	0.83[EUR][1000 genomes]
rs919245	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[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	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11742341	ADAMTS16	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5185200-5262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:5199000-5240000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:5200200-5252800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:5202600-5240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:5221600-5242200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:5222200-5244000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:5224400-5253800	Weak transcription	Fetal Kidney	kidney
8	chr5:5230200-5255400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:5232000-5245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:5234600-5252600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:5236800-5255400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:5237200-5242800	Strong transcription	Ovary	ovary
13	chr5:5238000-5250200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:5238400-5246000	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:5239000-5240000	Strong transcription	NH-A	brain
16	chr5:5239000-5246600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:5239200-5240800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr5:5239200-5245400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:5239400-5263000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:5239600-5240800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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