Variant report

Variant	rs12539174
Chromosome Location	chr7:16127297-16127298
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:16113784..16116426-chr7:16125295..16127374,2	K562	blood:
2	chr7:16127250..16129202-chr7:16129433..16131749,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ISPD-1	chr7:16127152-16129275	ENSG00000273477.1

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10227232	0.85[CEU][hapmap]
rs1034959	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs10487911	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950601	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10950604	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11760631	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11760717	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11762563	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11773181	1.00[YRI][hapmap]
rs11773533	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12533693	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12537658	0.82[EUR][1000 genomes]
rs12539945	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12667418	0.84[EUR][1000 genomes]
rs12699769	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13221870	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13231996	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13245773	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1405591	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1527203	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1527205	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17169263	1.00[YRI][hapmap]
rs17284967	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008133	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2240855	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28444529	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34612021	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66933521	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6960138	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs73071843	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs758702	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7777809	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785638	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7794107	0.82[YRI][hapmap]
rs7801576	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv949309	chr7:15986709-16236162	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv949555	chr7:16078412-16279290	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539174	TMEM106B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16118200-16129400	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:16122200-16133000	Weak transcription	Psoas Muscle	Psoas
3	chr7:16122400-16135400	Weak transcription	Left Ventricle	heart
4	chr7:16124400-16127400	Enhancers	HUVEC	blood vessel
5	chr7:16124400-16131400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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