Variant report

Variant	rs12658487
Chromosome Location	chr5:5221568-5221569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12652633	0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12660007	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13186769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2399736	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399737	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2913616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2913618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2913619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2913620	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2913623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2913624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964439	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34819663	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4702250	0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs67447053	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs12658487	ADAMTS16	cis	cerebellum	SCAN

Chromatin state (count:26 , 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	chr5:5199800-5228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:5200200-5252800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:5201400-5223000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:5201400-5226000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:5202600-5240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:5205400-5222400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:5209600-5222000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:5218400-5222600	Weak transcription	Fetal Kidney	kidney
11	chr5:5220400-5221600	Enhancers	Fetal Muscle Trunk	muscle
12	chr5:5220600-5221600	Enhancers	Psoas Muscle	Psoas
13	chr5:5220600-5221800	Enhancers	HSMMtube	muscle
14	chr5:5220600-5222400	Enhancers	Fetal Muscle Leg	muscle
15	chr5:5220800-5222000	Enhancers	HSMM	muscle
16	chr5:5220800-5222400	Enhancers	NH-A	brain
17	chr5:5221000-5221600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:5221000-5221800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:5221000-5222400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:5221000-5222400	Enhancers	Fetal Stomach	stomach
21	chr5:5221200-5222000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:5221200-5222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:5221400-5221600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr5:5221400-5221600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr5:5221400-5222000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:5221400-5237200	Weak transcription	Ovary	ovary

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