Variant report

Variant	rs6547705
Chromosome Location	chr2:87044316-87044317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10186663	0.88[MEX][hapmap]
rs10201422	0.88[MEX][hapmap]
rs10209550	0.89[ASN][1000 genomes]
rs1049457	0.83[MEX][hapmap]
rs1049458	0.88[MEX][hapmap]
rs1193	0.88[MEX][hapmap]
rs12714202	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs13010845	0.89[ASN][1000 genomes]
rs1400032	0.89[ASN][1000 genomes]
rs1878109	0.83[MEX][hapmap]
rs2063848	0.83[MEX][hapmap]
rs2271666	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2367378	0.88[MEX][hapmap]
rs28527279	0.89[ASN][1000 genomes]
rs2887012	0.83[MEX][hapmap]
rs308917	0.89[ASN][1000 genomes]
rs308918	0.89[ASN][1000 genomes]
rs4832049	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4832307	0.89[ASN][1000 genomes]
rs4832311	0.83[MEX][hapmap]
rs6705448	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs6726451	0.88[MEX][hapmap]
rs6731890	0.83[MEX][hapmap]
rs6743139	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs6750263	0.89[ASN][1000 genomes]
rs7579919	0.83[AMR][1000 genomes]
rs9309636	0.83[MEX][hapmap]
rs9309637	0.83[MEX][hapmap]
rs9309638	0.83[MEX][hapmap]
rs938486	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv532319	chr2:87024867-88005418	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
16	nsv961427	chr2:87032925-87059989	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Progressive supranuclear palsy	21685912	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6547705	VPS24	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:87035600-87048800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:87037200-87048000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:87037200-87048800	Weak transcription	Esophagus	oesophagus
4	chr2:87037800-87045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:87040600-87046600	Enhancers	Fetal Intestine Large	intestine
6	chr2:87041000-87048600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:87042800-87045000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr2:87042800-87045400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:87042800-87045800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:87043000-87045000	Weak transcription	Small Intestine	intestine
11	chr2:87043400-87044400	Enhancers	Thymus	Thymus
12	chr2:87043400-87045400	Weak transcription	Dnd41	blood
13	chr2:87043600-87045600	Weak transcription	Primary T cells from cord blood	blood
14	chr2:87043600-87045600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:87043800-87045000	Strong transcription	Fetal Thymus	thymus
16	chr2:87043800-87045600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:87044200-87044400	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links