Variant report

Variant	rs2975002
Chromosome Location	chr17:18026980-18026981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:18019422..18021646-chr17:18026268..18029392,3	MCF-7	breast:
2	chr17:18025241..18027862-chr17:18084839..18087290,2	K562	blood:
3	chr17:18023938..18027022-chr17:18030857..18033750,4	MCF-7	breast:
4	chr17:18021481..18023947-chr17:18025054..18028164,3	MCF-7	breast:
5	chr17:18025526..18028279-chr17:18085788..18088431,2	MCF-7	breast:
6	chr17:18018156..18020480-chr17:18026722..18028730,2	K562	blood:
7	chr17:18014082..18015832-chr17:18026108..18028285,2	MCF-7	breast:
8	chr17:18026105..18028759-chr17:18029242..18030867,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2272570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2925139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2925140	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2925141	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2925142	0.88[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2925143	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2955361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2955362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2955363	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2955364	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955374	0.85[ASN][1000 genomes]
rs2955375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2955386	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2955387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2975000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2975001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2975003	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2975004	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2975005	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4513153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4925139	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502635	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7225972	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8077176	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2975002	ATPAF2	cis	Thyroid	GTEx
rs2975002	ATPAF2	cis	Muscle Skeletal	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18010600-18030400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:18025000-18028200	Enhancers	Fetal Muscle Leg	muscle
3	chr17:18025200-18028400	Enhancers	Fetal Lung	lung
4	chr17:18025800-18028000	Enhancers	Fetal Muscle Trunk	muscle
5	chr17:18026200-18027000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr17:18026200-18027000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr17:18026400-18027000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:18026400-18028000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:18026600-18027000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr17:18026600-18027400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:18026800-18027000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:18026800-18027600	Enhancers	Psoas Muscle	Psoas

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