Variant report

Variant	rs6479456
Chromosome Location	chr9:95909429-95909430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10114849	0.87[AMR][1000 genomes]
rs10739943	0.87[AMR][1000 genomes]
rs10992649	1.00[AFR][1000 genomes]
rs10992654	1.00[AFR][1000 genomes]
rs10992656	1.00[AFR][1000 genomes]
rs12378451	1.00[ASW][hapmap]
rs1419232	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs1936400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2398824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2398826	0.95[EUR][1000 genomes]
rs2398830	0.91[ASN][1000 genomes]
rs4335184	0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743886	1.00[ASW][hapmap]
rs4743895	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744179	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744180	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479455	0.87[AMR][1000 genomes]
rs7867718	0.87[AMR][1000 genomes]
rs7875586	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6479456	PHF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95899800-95922200	Weak transcription	Gastric	stomach
2	chr9:95904800-95911600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:95906800-95910000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr9:95907000-95911000	Weak transcription	Aorta	Aorta
5	chr9:95907200-95910000	Weak transcription	Psoas Muscle	Psoas
6	chr9:95907200-95913200	Weak transcription	HepG2	liver
7	chr9:95907200-95913400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:95907200-95918600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:95907200-95922200	Weak transcription	Pancreas	Pancrea
10	chr9:95907200-95944400	Weak transcription	Right Atrium	heart
11	chr9:95907400-95911400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:95907400-95911400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:95908600-95911400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:95908600-95918600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:95909000-95911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:95909200-95909600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr9:95909400-95909600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:95909400-95910000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:95909400-95922000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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