Variant report

Variant	rs17015268
Chromosome Location	chr1:209988989-209988990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209969439..209971872-chr1:209988283..209991092,2	MCF-7	breast:
2	chr1:209986093..209989854-chr1:209998017..210002656,5	K562	blood:
3	chr1:209988063..209993866-chr1:209997170..210003138,6	MCF-7	breast:
4	chr1:209987591..209990855-chr1:209991529..209994207,3	K562	blood:

Variant related genes	Relation type
ENSG00000117597	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119345	0.91[AMR][1000 genomes]
rs11119346	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12075674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs12405750	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2069068	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes]
rs2235370	0.85[AMR][1000 genomes]
rs2235371	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs3753517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4844491	1.00[AFR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844496	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17015268	SNORD117	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209979800-209989200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:209981800-209989200	Weak transcription	Esophagus	oesophagus
3	chr1:209981800-209989600	Weak transcription	Spleen	Spleen
4	chr1:209981800-209989800	Weak transcription	Right Atrium	heart
5	chr1:209982000-209989200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:209982400-209989200	Weak transcription	Placenta	Placenta
7	chr1:209984400-209989200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:209985400-209989200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209987800-209989000	Enhancers	NHEK	skin
10	chr1:209987800-209989200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:209987800-209989200	Enhancers	HMEC	breast
12	chr1:209987800-209991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209988000-209991400	Enhancers	Fetal Thymus	thymus
14	chr1:209988200-209989200	Weak transcription	HepG2	liver
15	chr1:209988800-209989200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:209988800-209989400	Enhancers	Primary T helper cells PMA-I stimulated	--

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