Variant report

Variant	rs12239017
Chromosome Location	chr1:212886860-212886861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10127613	0.85[EUR][1000 genomes]
rs1032964	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10779582	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10779583	0.82[EUR][1000 genomes]
rs10863992	0.82[EUR][1000 genomes]
rs10864002	0.81[EUR][1000 genomes]
rs11120005	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120034	0.81[EUR][1000 genomes]
rs12568552	0.84[EUR][1000 genomes]
rs12744555	0.81[EUR][1000 genomes]
rs12757944	0.81[EUR][1000 genomes]
rs1507359	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs15702	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1580991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813705	0.83[EUR][1000 genomes]
rs1848243	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2292214	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2884675	0.81[EUR][1000 genomes]
rs3738802	0.84[EUR][1000 genomes]
rs3949369	0.81[EUR][1000 genomes]
rs4548508	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4639827	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4951458	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4951639	0.84[EUR][1000 genomes]
rs6540754	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6540766	0.83[EUR][1000 genomes]
rs6540767	0.81[EUR][1000 genomes]
rs6665489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670373	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670869	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6678961	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686164	0.84[EUR][1000 genomes]
rs6688947	0.97[ASN][1000 genomes]
rs6694887	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6696908	0.83[AMR][1000 genomes]
rs6700465	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6702544	0.84[EUR][1000 genomes]
rs6703982	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513199	0.87[EUR][1000 genomes]
rs7513210	0.87[EUR][1000 genomes]
rs7513734	0.88[EUR][1000 genomes]
rs7513772	0.88[EUR][1000 genomes]
rs7514070	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7522100	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7528303	0.81[EUR][1000 genomes]
rs7535608	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7538853	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7543603	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7547100	0.88[EUR][1000 genomes]
rs7555930	0.84[EUR][1000 genomes]
rs9651103	0.93[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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12239017	FLVCR1-AS1	cis	Whole Blood	GTEx
rs12239017	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12239017	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs12239017	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212886200-212887200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:212886400-212891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:212886400-212894400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:212886600-212894400	Weak transcription	Osteobl	bone
5	chr1:212886800-212887000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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