Variant report

Variant	rs12659143
Chromosome Location	chr5:95591317-95591318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10476546	0.86[CEU][hapmap]
rs10866767	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11135450	0.86[CEU][hapmap]
rs11135457	1.00[YRI][hapmap]
rs11741888	0.87[CHB][hapmap]
rs11743265	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[YRI][hapmap]
rs11747615	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11948972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11959068	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13153770	0.86[AMR][1000 genomes]
rs13178392	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13181198	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1995186	0.82[EUR][1000 genomes]
rs34023054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34639000	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34713740	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34973883	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792744	1.00[YRI][hapmap]
rs3811942	1.00[ASW][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs3922467	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4424016	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4529218	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4637573	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4869276	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4869284	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs62367170	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866846	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7444135	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7710625	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv882390	chr5:95486940-95591580	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv830410	chr5:95505799-95666310	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12659143	ERAP2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95583200-95595200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:95583800-95595000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:95583800-95595000	Weak transcription	Psoas Muscle	Psoas
4	chr5:95584000-95592400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:95585000-95594600	Weak transcription	HepG2	liver
6	chr5:95586200-95591400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:95586200-95595000	Weak transcription	Pancreas	Pancrea
8	chr5:95587800-95595400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:95588000-95592000	Enhancers	HMEC	breast
10	chr5:95588200-95596600	Enhancers	HUVEC	blood vessel
11	chr5:95588400-95596000	Enhancers	Osteobl	bone
12	chr5:95589400-95592000	Enhancers	NHEK	skin
13	chr5:95589600-95591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:95589800-95596800	Enhancers	HSMM	muscle
15	chr5:95590000-95595600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:95590200-95591800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:95590200-95592000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:95590200-95593200	Enhancers	NHLF	lung
19	chr5:95590400-95591800	Flanking Active TSS	A549	lung
20	chr5:95590600-95591600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:95590600-95591800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:95590600-95591800	Enhancers	HSMMtube	muscle
23	chr5:95590800-95591400	Enhancers	Stomach Mucosa	stomach
24	chr5:95590800-95591600	Enhancers	Fetal Lung	lung
25	chr5:95590800-95591800	Enhancers	Adipose Nuclei	Adipose
26	chr5:95590800-95591800	Flanking Active TSS	NHDF-Ad	bronchial
27	chr5:95590800-95592000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:95591200-95591400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:95591200-95591400	Enhancers	NH-A	brain
30	chr5:95591200-95591600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr5:95591200-95591800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95591200-95592000	Enhancers	Hela-S3	cervix
33	chr5:95591200-95595200	Weak transcription	Aorta	Aorta
34	chr5:95591200-95595800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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