Variant report

Variant	rs17025241
Chromosome Location	chr3:88053396-88053397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10511136	0.81[CEU][hapmap]
rs11717021	0.81[ASN][1000 genomes]
rs12714696	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13074576	0.88[ASN][1000 genomes]
rs1431153	0.88[ASN][1000 genomes]
rs1503433	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1604699	0.83[ASN][1000 genomes]
rs17025236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17549345	0.81[CEU][hapmap]
rs1835542	0.88[ASN][1000 genomes]
rs1835543	0.88[ASN][1000 genomes]
rs2016224	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2082226	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099229	0.83[ASN][1000 genomes]
rs2344185	0.81[CEU][hapmap]
rs2880801	0.81[ASN][1000 genomes]
rs2880802	0.83[ASN][1000 genomes]
rs35040143	0.88[ASN][1000 genomes]
rs4858925	0.84[ASN][1000 genomes]
rs4858969	0.84[ASN][1000 genomes]
rs4858971	0.88[ASN][1000 genomes]
rs4858972	0.85[ASN][1000 genomes]
rs4858974	0.88[ASN][1000 genomes]
rs4858975	0.88[ASN][1000 genomes]
rs56006017	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56173847	0.84[EUR][1000 genomes]
rs56323967	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58658187	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67566069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770013	0.84[ASN][1000 genomes]
rs6778211	0.84[ASN][1000 genomes]
rs6781226	0.84[ASN][1000 genomes]
rs6781901	0.88[ASN][1000 genomes]
rs6787253	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798161	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6804199	0.84[EUR][1000 genomes]
rs6804848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68068970	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73140133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140134	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73144053	0.83[EUR][1000 genomes]
rs7629565	0.88[ASN][1000 genomes]
rs7630716	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7652406	0.88[ASN][1000 genomes]
rs9310061	0.88[ASN][1000 genomes]
rs9681975	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852704	0.81[CEU][hapmap]
rs9855839	0.88[ASN][1000 genomes]
rs9859034	0.84[CEU][hapmap]
rs9861809	0.88[ASN][1000 genomes]
rs9863076	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9878862	0.88[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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv536635	chr3:88049304-88088520	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17025241	HTR1F	cis	parietal	SCAN
rs17025241	CGGBP1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88046800-88054400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:88048600-88054200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:88050400-88054200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:88050400-88054400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:88050600-88054000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:88050600-88054200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:88050600-88054200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:88052800-88054000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links