Variant report

Variant	rs12038888
Chromosome Location	chr1:212366053-212366054
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212359998..212362512-chr1:212365289..212368132,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1009622	0.80[CHB][hapmap]
rs10436962	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10436976	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119880	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119884	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs11119885	0.80[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs11119887	0.93[EUR][1000 genomes]
rs12041554	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs12746096	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389369	0.80[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs1389370	0.81[EUR][1000 genomes]
rs1472226	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2012917	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs2087946	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2307128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2358452	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs351386	0.80[CHB][hapmap]
rs35209719	0.81[EUR][1000 genomes]
rs3816912	0.82[EUR][1000 genomes]
rs4362041	0.80[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs4500383	0.83[EUR][1000 genomes]
rs6540731	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6540732	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs6540733	0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs6540734	0.81[EUR][1000 genomes]
rs6540735	0.81[EUR][1000 genomes]
rs6657900	0.80[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs6668866	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs6679064	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6679796	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs7515645	0.82[EUR][1000 genomes]
rs7519168	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7542973	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7544225	0.80[CHB][hapmap]
rs903120	0.80[EUR][1000 genomes]
rs903121	0.83[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs951623	0.82[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12038888	TMEM206	cis	Esophagus Mucosa	GTEx
rs12038888	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212363600-212368600	Weak transcription	Lung	lung
2	chr1:212365600-212366400	Enhancers	HepG2	liver
3	chr1:212366000-212369600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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