Variant report

Variant	rs12200412
Chromosome Location	chr6:44848184-44848185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10456119	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10484627	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10948183	0.86[ASN][1000 genomes]
rs10948185	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10948186	0.84[ASN][1000 genomes]
rs1150806	0.81[ASN][1000 genomes]
rs11524119	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11525038	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12191518	0.83[ASN][1000 genomes]
rs12197442	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12198904	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12207620	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12209076	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12524069	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12525009	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12526711	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1293598	0.87[ASN][1000 genomes]
rs1293600	0.80[ASN][1000 genomes]
rs13201202	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13211229	0.81[EUR][1000 genomes]
rs13213412	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13215618	0.83[ASN][1000 genomes]
rs1578676	0.84[ASN][1000 genomes]
rs1590864	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17422760	0.86[ASN][1000 genomes]
rs34808716	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34982599	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3778507	0.83[ASN][1000 genomes]
rs3799971	0.82[ASN][1000 genomes]
rs3799973	0.83[ASN][1000 genomes]
rs3799976	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799977	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799979	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799981	0.87[ASN][1000 genomes]
rs3799984	0.82[ASN][1000 genomes]
rs3799986	0.84[ASN][1000 genomes]
rs3846896	0.84[ASN][1000 genomes]
rs3957281	0.88[ASN][1000 genomes]
rs4711803	0.86[ASN][1000 genomes]
rs4711805	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711807	0.80[EUR][1000 genomes]
rs4714828	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs472672	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs472673	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs500773	0.86[ASN][1000 genomes]
rs538801	0.86[ASN][1000 genomes]
rs567054	0.86[ASN][1000 genomes]
rs588848	0.86[ASN][1000 genomes]
rs591129	0.80[ASN][1000 genomes]
rs608941	0.86[ASN][1000 genomes]
rs62438007	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62438011	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458414	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6458415	0.83[ASN][1000 genomes]
rs679713	0.84[ASN][1000 genomes]
rs6903576	0.86[ASN][1000 genomes]
rs6923519	0.86[ASN][1000 genomes]
rs718112	0.87[ASN][1000 genomes]
rs7747642	0.87[ASN][1000 genomes]
rs7749865	0.80[ASN][1000 genomes]
rs7754378	0.87[ASN][1000 genomes]
rs7763421	0.87[ASN][1000 genomes]
rs9367211	0.85[ASN][1000 genomes]
rs9369516	0.84[ASN][1000 genomes]
rs9395051	0.82[ASN][1000 genomes]
rs9395055	0.85[ASN][1000 genomes]
rs9472407	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033815	chr6:44845514-44938799	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12200412	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44833600-44849400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:44838200-44848800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:44838400-44854200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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