Variant report

Variant	rs16825519
Chromosome Location	chr1:186504772-186504773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10489396	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs10489397	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10911877	0.82[JPT][hapmap]
rs1108635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11799322	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11800288	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11800338	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11800651	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11801527	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11801617	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11802705	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11803944	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11803969	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11804161	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11804785	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11805289	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11805597	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11806017	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11806304	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11806329	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11806663	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11806701	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807318	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807443	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807927	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11808165	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11808643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11809088	0.84[EUR][1000 genomes]
rs11809402	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11810534	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11811259	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11811260	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11811320	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs11811335	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12723621	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12726528	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12726764	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12731288	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12731687	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12733799	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs12739006	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12739643	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12739797	0.88[CHD][hapmap];0.92[TSI][hapmap]
rs12740221	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12742751	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12747113	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12747991	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12750686	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12752376	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12753223	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12754662	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16825361	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16825403	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16825434	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16825473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16825600	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1883650	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1919194	0.94[JPT][hapmap]
rs2008704	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2206974	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2223783	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2223784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2383509	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2383512	0.82[EUR][1000 genomes]
rs2383513	0.84[EUR][1000 genomes]
rs2383514	0.84[EUR][1000 genomes]
rs2891249	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33963275	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33996079	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34200789	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34228564	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34249733	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34272627	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34310508	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34459464	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34513409	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34578387	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34778311	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34781399	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34783173	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34858233	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35205448	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35206897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35240980	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326401	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35461575	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35481005	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35636342	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35868587	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35945739	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36016361	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36030781	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36053737	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766698	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs3766701	1.00[ASW][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs3901243	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3933210	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4140432	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4140434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58626385	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6674145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677346	0.82[JPT][hapmap]
rs6678198	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6680055	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6682896	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683271	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71634161	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71634164	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71634167	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71634173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71634175	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71634176	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16825519	OCLM	cis	cerebellum	SCAN
rs16825519	C1orf14	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186501400-186505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:186501600-186505600	Weak transcription	HSMMtube	muscle
3	chr1:186503600-186507600	Enhancers	NHDF-Ad	bronchial
4	chr1:186503800-186505200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:186503800-186508000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:186504000-186504800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:186504000-186505000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:186504000-186506200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:186504000-186506400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:186504000-186506400	Enhancers	NH-A	brain
11	chr1:186504000-186506800	Enhancers	Osteobl	bone
12	chr1:186504000-186507200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:186504000-186507400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:186504400-186506000	Enhancers	NHEK	skin
15	chr1:186504400-186506600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:186504600-186504800	Enhancers	Right Atrium	heart
17	chr1:186504600-186504800	Enhancers	A549	lung
18	chr1:186504600-186504800	Flanking Active TSS	HUVEC	blood vessel
19	chr1:186504600-186505000	Enhancers	Brain Angular Gyrus	brain
20	chr1:186504600-186505000	Enhancers	Brain Hippocampus Middle	brain
21	chr1:186504600-186505000	Enhancers	Fetal Muscle Leg	muscle
22	chr1:186504600-186505200	Enhancers	Adipose Nuclei	Adipose
23	chr1:186504600-186505200	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:186504600-186505600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:186504600-186506000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:186504600-186506000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:186504600-186506200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:186504600-186506200	Enhancers	Hela-S3	cervix
29	chr1:186504600-186506400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:186504600-186506400	Enhancers	HMEC	breast
31	chr1:186504600-186506400	Enhancers	NHLF	lung
32	chr1:186504600-186507400	Enhancers	Muscle Satellite Cultured Cells	--

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