Variant report

Variant	rs9904644
Chromosome Location	chr17:33878224-33878225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:33878180-33878330	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:33870813..33874326-chr17:33876261..33879859,4	K562	blood:
2	chr17:33877720..33881405-chr17:33884956..33887272,3	K562	blood:
3	chr17:33872306..33875717-chr17:33876855..33878758,3	K562	blood:

Variant related genes	Relation type
ENSG00000267359	TF binding region
ENSG00000236320	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001441	0.94[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs1037591	0.82[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs10491114	0.86[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs1071965	0.86[AMR][1000 genomes]
rs11870472	0.91[AMR][1000 genomes]
rs12452633	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12600662	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs16971117	0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16971122	0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1964509	0.91[AFR][1000 genomes]
rs226424	1.00[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs226427	0.82[JPT][hapmap]
rs226433	0.86[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs226435	0.86[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs226436	1.00[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs2278950	1.00[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs28361509	0.89[AFR][1000 genomes]
rs28384428	0.86[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs3760325	0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs3785759	0.84[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7211363	0.88[AFR][1000 genomes]
rs9303689	0.86[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs9907911	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574754	chr17:33841737-33881631	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9904644	SNORD116-29	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33870400-33881000	Weak transcription	K562	blood
2	chr17:33870400-33888600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:33873800-33879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:33874000-33878600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:33874200-33878800	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