Variant report

Variant	rs4715016
Chromosome Location	chr6:12963962-12963963
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	chr6:12958071..12959752-chr6:12963422..12965473,2	K562	blood:

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11757634	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[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961007	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11963982	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13207062	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1937768	0.82[JPT][hapmap]
rs4236091	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4349811	0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs4380742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711899	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4715023	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[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715032	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715043	0.96[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4715048	0.80[AMR][1000 genomes]
rs6458568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900619	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901563	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6916268	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6920970	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7341250	0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs7739717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7743219	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7760857	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7762881	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7770277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7774403	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7774775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296556	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296580	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9369768	0.82[CHD][hapmap]
rs9381636	0.86[CHD][hapmap];0.81[GIH][hapmap]
rs9463337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9463363	0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes]
rs9463364	0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs9473113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9473156	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9473188	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9473198	0.87[AMR][1000 genomes]

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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4715016	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12959200-12964000	Enhancers	Brain Cingulate Gyrus	brain
2	chr6:12959200-12968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:12961000-12968400	Weak transcription	Brain Substantia Nigra	brain
4	chr6:12962000-12964000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr6:12962000-12964400	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:12962200-12964000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:12962200-12964200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:12962400-12964000	Enhancers	Adipose Nuclei	Adipose
9	chr6:12962400-12966200	Weak transcription	Lung	lung
10	chr6:12962600-12964000	Flanking Active TSS	HUVEC	blood vessel
11	chr6:12962800-12964200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr6:12962800-12964200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:12962800-12968000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:12963000-12964000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:12963000-12964000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:12963000-12964200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:12963000-12967400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:12963200-12967800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:12963400-12964000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:12963400-12967800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:12963600-12964000	Enhancers	Stomach Smooth Muscle	stomach
22	chr6:12963600-12964200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:12963600-12966600	Weak transcription	Brain Germinal Matrix	brain
24	chr6:12963600-12967200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:12963600-12967600	Weak transcription	NHDF-Ad	bronchial
26	chr6:12963600-12969400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:12963600-12971000	Weak transcription	HSMM	muscle
28	chr6:12963600-12971600	Weak transcription	Spleen	Spleen
29	chr6:12963600-12972400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:12963600-12973000	Weak transcription	Pancreas	Pancrea
31	chr6:12963600-12974600	Weak transcription	Right Ventricle	heart
32	chr6:12963800-12964000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:12963800-12964000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr6:12963800-12964000	Flanking Active TSS	Fetal Heart	heart
35	chr6:12963800-12964000	Flanking Active TSS	Left Ventricle	heart
36	chr6:12963800-12964000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:12963800-12964200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:12963800-12964200	Enhancers	Fetal Lung	lung
39	chr6:12963800-12964600	Weak transcription	Aorta	Aorta

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