Variant report

Variant	rs3799978
Chromosome Location	chr6:44837532-44837533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1041333	0.82[EUR][1000 genomes]
rs10948186	0.82[EUR][1000 genomes]
rs10948187	0.83[EUR][1000 genomes]
rs10948190	0.82[EUR][1000 genomes]
rs10948194	0.83[EUR][1000 genomes]
rs10948195	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12191518	0.82[EUR][1000 genomes]
rs1293598	0.83[EUR][1000 genomes]
rs1360196	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1576382	0.83[EUR][1000 genomes]
rs1854547	0.83[EUR][1000 genomes]
rs1935551	0.88[EUR][1000 genomes]
rs2145826	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs227837	0.80[AMR][1000 genomes]
rs227838	0.80[AMR][1000 genomes]
rs2396370	0.83[EUR][1000 genomes]
rs2396371	0.81[EUR][1000 genomes]
rs2396373	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3778507	0.83[EUR][1000 genomes]
rs3799967	0.88[EUR][1000 genomes]
rs3799968	0.88[EUR][1000 genomes]
rs3799971	0.88[EUR][1000 genomes]
rs3846896	0.90[EUR][1000 genomes]
rs494982	0.81[EUR][1000 genomes]
rs57020561	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636845	0.80[EUR][1000 genomes]
rs6458415	0.86[EUR][1000 genomes]
rs6903576	0.88[EUR][1000 genomes]
rs6904015	0.88[EUR][1000 genomes]
rs6910294	0.88[EUR][1000 genomes]
rs6910749	0.80[EUR][1000 genomes]
rs6919485	0.82[EUR][1000 genomes]
rs6923519	0.87[EUR][1000 genomes]
rs6940547	0.81[EUR][1000 genomes]
rs7754698	0.87[EUR][1000 genomes]
rs929614	0.80[EUR][1000 genomes]
rs9296448	0.84[EUR][1000 genomes]
rs9349303	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9357459	0.88[EUR][1000 genomes]
rs9357464	0.82[EUR][1000 genomes]
rs9367208	0.89[EUR][1000 genomes]
rs9367211	0.87[EUR][1000 genomes]
rs9369512	0.85[EUR][1000 genomes]
rs9369513	0.88[EUR][1000 genomes]
rs9369514	0.90[EUR][1000 genomes]
rs9369515	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9369516	0.89[EUR][1000 genomes]
rs9369523	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9381359	0.81[EUR][1000 genomes]
rs9395051	0.89[EUR][1000 genomes]
rs9395055	0.86[EUR][1000 genomes]
rs9463054	0.84[EUR][1000 genomes]
rs9463055	0.83[EUR][1000 genomes]
rs9472383	0.87[EUR][1000 genomes]
rs9472403	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472418	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs976699	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799978	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44828400-44837800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:44833600-44849400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:44836000-44838000	Flanking Active TSS	GM12878-XiMat	blood
4	chr6:44836600-44837800	Enhancers	Fetal Intestine Small	intestine
5	chr6:44836600-44838000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:44837000-44838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:44837200-44838200	Enhancers	HepG2	liver
8	chr6:44837400-44837600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:44837400-44837800	Enhancers	Fetal Heart	heart
10	chr6:44837400-44837800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links