Variant report

Variant	rs10489397
Chromosome Location	chr1:186598610-186598611
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186343972..186347351-chr1:186596243..186599191,3	K562	blood:
2	chr1:186598408..186600581-chr1:186603611..186606250,2	K562	blood:

Variant related genes	Relation type
ENSG00000157181	Chromatin interaction
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10489396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911895	0.81[ASN][1000 genomes]
rs10911899	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1108635	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11799322	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11800288	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11800338	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11800651	0.80[AMR][1000 genomes]
rs11801527	0.85[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs11801617	0.90[EUR][1000 genomes]
rs11802553	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11802705	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11803944	0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs11803969	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11804161	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11804785	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11805597	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11806017	0.82[AMR][1000 genomes]
rs11806329	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11806663	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11806701	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11807318	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807443	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807927	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11808165	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11808643	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11808900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809088	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11810534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811047	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11811259	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811260	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811335	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12239058	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12723621	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12726528	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12726764	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12731288	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12731687	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12734267	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12734420	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12739006	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12739643	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12747113	0.82[AMR][1000 genomes]
rs12747991	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12750686	0.82[AMR][1000 genomes]
rs12752376	0.80[AMR][1000 genomes]
rs12753223	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12754662	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16825361	0.82[AMR][1000 genomes]
rs16825403	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs16825434	0.82[AMR][1000 genomes]
rs16825473	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16825519	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16825600	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16825639	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16825646	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16825671	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16825681	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16825687	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1883650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883651	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1883652	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2008704	0.83[AMR][1000 genomes]
rs2206974	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223783	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223784	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2383509	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2383512	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2383513	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2383514	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2891249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2891250	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33963275	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs33996079	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34101282	0.81[EUR][1000 genomes]
rs34200789	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34228564	0.82[AMR][1000 genomes]
rs34249733	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34272627	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34310508	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34365031	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34459464	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34513409	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34578387	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34770837	0.86[EUR][1000 genomes]
rs34778311	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34781399	0.82[AMR][1000 genomes]
rs34783173	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34858233	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35084661	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35205448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206897	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35240980	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35326401	0.82[AMR][1000 genomes]
rs35461575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35481005	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35483551	0.85[EUR][1000 genomes]
rs35636342	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35868587	0.85[AMR][1000 genomes]
rs35945739	0.80[AMR][1000 genomes]
rs36016361	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36030781	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36053737	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3901243	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3933210	0.82[AMR][1000 genomes]
rs4140432	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140434	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4511065	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58626385	0.82[AMR][1000 genomes]
rs6674145	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6678198	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680055	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6682896	1.00[CEU][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs6683271	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689466	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs71634161	0.82[AMR][1000 genomes]
rs71634164	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs71634167	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71634173	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71634175	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71634176	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71634178	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71634179	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71634186	0.90[EUR][1000 genomes];0.87[ASN][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	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
4	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489397	OCLM	cis	cerebellum	SCAN
rs10489397	C1orf14	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186592600-186602000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:186593200-186600200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:186595200-186599000	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:186597800-186599200	Enhancers	Colon Smooth Muscle	Colon
5	chr1:186598200-186598800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:186598200-186599000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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