Variant report

Variant	rs4779046
Chromosome Location	chr15:83342772-83342773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83342701..83346564-chr15:83347481..83349539,4	MCF-7	breast:
2	chr15:83331639..83335062-chr15:83341237..83342971,3	K562	blood:
3	chr15:83331639..83334296-chr15:83341463..83342971,2	K562	blood:

Variant related genes	Relation type
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1105867	0.82[YRI][hapmap]
rs1145170	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap]
rs1259176	0.83[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12908713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313494	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs1553885	0.95[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs17356528	0.88[ASN][1000 genomes]
rs2567632	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34940771	0.84[ASN][1000 genomes]
rs4779051	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4779052	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62009945	0.91[ASN][1000 genomes]
rs6422424	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163840	0.91[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7165129	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178459	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs783524	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs783528	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs783538	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs783541	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs803686	0.89[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv1808975	chr15:83307574-83360168	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4779046	RASGRF1	cis	cerebellum	SCAN
rs4779046	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs4779046	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs4779046	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL
rs4779046	RP11-152F13.7	cis	lung	GTEx
rs4779046	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs4779046	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs4779046	YES1	trans	lymphoblastoid	RTeQTL
rs4779046	SCARNA15	cis	lymphoblastoid	seeQTL
rs4779046	BTBD1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83331400-83346600	Weak transcription	Fetal Brain Male	brain
2	chr15:83334600-83342800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:83334800-83344400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:83335200-83349200	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:83335600-83344200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:83335800-83343200	Weak transcription	Brain Anterior Caudate	brain
7	chr15:83336800-83348200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:83337400-83342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:83337800-83343600	Weak transcription	Fetal Brain Female	brain
10	chr15:83340200-83348600	Weak transcription	Pancreas	Pancrea
11	chr15:83340600-83348600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:83341600-83345600	Strong transcription	Brain Germinal Matrix	brain
13	chr15:83342600-83343000	Strong transcription	Brain Angular Gyrus	brain
14	chr15:83342600-83343000	Enhancers	Brain Substantia Nigra	brain
15	chr15:83342600-83343400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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