Variant report

Variant	rs17272966
Chromosome Location	chr19:53739958-53739959
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	ZNF274	chr19:53739663-53741983	K562	blood:	n/a	n/a
2	ZNF274	chr19:53739762-53741340	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000269288	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10401578	0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs10404048	0.87[CHB][hapmap]
rs10425196	0.85[ASN][1000 genomes]
rs10775558	0.88[CHB][hapmap];0.89[CHD][hapmap]
rs10853858	0.86[CHD][hapmap]
rs10853859	0.88[CHB][hapmap]
rs11084227	0.94[CHB][hapmap];0.89[CHD][hapmap];0.86[LWK][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs11084228	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666631	0.92[ASN][1000 genomes]
rs12972588	0.89[ASN][1000 genomes]
rs12982260	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985503	0.88[ASN][1000 genomes]
rs28411117	0.97[ASN][1000 genomes]
rs2865241	0.93[ASN][1000 genomes]
rs28734122	0.85[ASN][1000 genomes]
rs2914371	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914372	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2914376	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914377	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914381	0.87[CHB][hapmap]
rs2914383	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914384	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2965221	0.87[CHB][hapmap]
rs2965222	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965223	0.87[CHB][hapmap]
rs2965224	0.87[CHB][hapmap]
rs2965230	0.86[CHB][hapmap]
rs2965231	0.87[CHB][hapmap]
rs2965236	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965237	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965238	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965240	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965242	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965243	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2965244	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3097248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111319	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36114232	0.85[ASN][1000 genomes]
rs4801965	0.87[CHB][hapmap]
rs4801968	0.81[CHB][hapmap]
rs4801970	0.88[CHB][hapmap]
rs4803069	0.85[ASN][1000 genomes]
rs4803071	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4803078	0.93[YRI][hapmap]
rs4803080	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779655	0.98[ASN][1000 genomes]
rs62117791	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs71363315	0.82[ASN][1000 genomes]
rs7247982	0.87[CHB][hapmap]
rs8113436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788	0.87[CHB][hapmap]

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	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1064604	chr19:53730688-53751243	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv580079	chr19:53732590-53756120	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17272966	ZNF418	cis	cerebellum	SCAN
rs17272966	ZNF304	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53728200-53748800	ZNF genes & repeats	Liver	Liver
2	chr19:53733600-53755200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:53733600-53755800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:53735800-53756200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:53736200-53749000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:53737800-53743000	Weak transcription	Pancreas	Pancrea
8	chr19:53738000-53743000	Weak transcription	Fetal Stomach	stomach
9	chr19:53738600-53740400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:53738600-53749000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:53738800-53756600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:53739000-53740400	Weak transcription	Fetal Brain Male	brain
13	chr19:53739000-53742000	ZNF genes & repeats	Psoas Muscle	Psoas
14	chr19:53739400-53743400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:53739400-53755200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:53739600-53740600	Weak transcription	Placenta	Placenta
17	chr19:53739600-53748600	ZNF genes & repeats	Brain Anterior Caudate	brain
18	chr19:53739600-53748600	ZNF genes & repeats	Brain Germinal Matrix	brain
19	chr19:53739600-53756200	ZNF genes & repeats	Fetal Brain Female	brain
20	chr19:53739800-53740400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links