Variant report

Variant	rs8039005
Chromosome Location	chr15:33372568-33372569
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33364817..33369587-chr15:33370489..33373626,4	MCF-7	breast:
2	chr15:33356120..33364271-chr15:33368982..33380679,29	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1026752	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519781	0.92[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519788	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775202	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10851823	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072170	0.84[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072175	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072187	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11636433	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639303	0.92[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857866	0.85[JPT][hapmap]
rs12439012	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440002	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235533	0.92[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235547	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17816711	1.00[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2219159	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2291064	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291065	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291066	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306278	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28510826	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551066	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28576977	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28603193	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28718544	0.96[ASN][1000 genomes]
rs345794	0.93[ASN][1000 genomes]
rs4779604	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779605	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779606	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4780074	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs922510	0.92[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922511	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8039005	FMN1	cis	Esophagus Mucosa	GTEx
rs8039005	FAN1	cis	parietal	SCAN
rs8039005	OCA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33361200-33378800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:33361600-33375600	Weak transcription	HSMM	muscle
3	chr15:33361800-33375600	Weak transcription	HSMMtube	muscle
4	chr15:33362000-33376000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:33362600-33375000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:33364000-33374000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:33368400-33373200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:33370400-33379200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:33370800-33377600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:33371800-33373400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:33372000-33372600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:33372000-33372800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:33372200-33372600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr15:33372200-33372600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr15:33372200-33372600	Enhancers	NHLF	lung
16	chr15:33372200-33373000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:33372400-33372600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr15:33372400-33372600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr15:33372400-33372600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:33372400-33374800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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