Variant report

Variant	rs236009
Chromosome Location	chr16:71251795-71251796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71250057..71252959-chr16:71321455..71323555,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180917	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11645087	0.82[TSI][hapmap]
rs11648802	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs12927616	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs146873	0.84[EUR][1000 genomes]
rs184647	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1859088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2015813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235990	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs235992	0.80[EUR][1000 genomes]
rs235995	0.82[EUR][1000 genomes]
rs235998	0.84[EUR][1000 genomes]
rs236003	0.84[EUR][1000 genomes]
rs236007	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236008	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236016	0.80[EUR][1000 genomes]
rs3094446	0.80[EUR][1000 genomes]
rs3114634	0.86[EUR][1000 genomes]
rs3743950	1.00[ASW][hapmap]
rs3785347	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs434108	0.80[EUR][1000 genomes]
rs443889	0.82[TSI][hapmap]
rs446245	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs6416727	0.83[JPT][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	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1060754	chr16:71008303-71276778	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs236009	NUTF2	cis	cerebellum	SCAN
rs236009	DHODH	cis	parietal	SCAN
rs236009	LCAT	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71248400-71252400	Enhancers	Brain Germinal Matrix	brain
2	chr16:71249000-71252000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:71249000-71252000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:71250800-71253200	Enhancers	Fetal Brain Male	brain
5	chr16:71251000-71252800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:71251000-71264200	Weak transcription	Pancreas	Pancrea
7	chr16:71251400-71251800	Enhancers	Fetal Stomach	stomach
8	chr16:71251400-71252000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr16:71251400-71252400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr16:71251400-71252600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr16:71251600-71252400	Flanking Active TSS	Fetal Brain Female	brain
12	chr16:71251600-71252800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:71251600-71253200	Enhancers	Brain Hippocampus Middle	brain

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