Variant report

Variant	rs7186852
Chromosome Location	chr16:30635659-30635660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr16:30634963-30635768	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000260113	TF binding region
ZNF689	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs12918327	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13338946	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs2289442	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs28728333	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841118	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919429	0.93[YRI][hapmap]
rs34699226	0.91[ASN][1000 genomes]
rs35629860	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs35661204	0.85[ASN][1000 genomes]
rs36063822	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs36064568	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747481	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs3747486	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs3812999	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs4485386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889490	1.00[CHD][hapmap]
rs55875685	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6565195	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565196	0.85[EUR][1000 genomes]
rs67693285	1.00[ASN][1000 genomes]
rs7184055	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7185620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187071	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187359	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs7187802	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7188789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7191389	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191761	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194347	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197475	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198250	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs7204632	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7499339	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046001	0.88[CHD][hapmap]
rs8058578	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs8058961	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs885107	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs9925025	0.83[ASW][hapmap];0.96[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9927137	1.00[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	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	19838193	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7186852	C16orf93	cis	parietal	SCAN
rs7186852	BCL7C	cis	cerebellum	SCAN
rs7186852	MYST1	cis	cerebellum	SCAN
rs7186852	DCTPP1	cis	cerebellum	SCAN
rs7186852	YPEL3	cis	cerebellum	SCAN
rs7186852	PHKG2	cis	parietal	SCAN
rs7186852	MYST1	cis	parietal	SCAN
rs7186852	ZNF768	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30631400-30640000	Weak transcription	Fetal Brain Male	brain
2	chr16:30631800-30640000	Weak transcription	Fetal Intestine Large	intestine
3	chr16:30632400-30636000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:30632600-30636200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:30633400-30636000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr16:30633800-30636000	Enhancers	K562	blood
7	chr16:30634200-30640000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:30634400-30640000	Weak transcription	Fetal Kidney	kidney
9	chr16:30634600-30636000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:30634600-30640000	Weak transcription	Fetal Intestine Small	intestine
11	chr16:30634600-30640000	Weak transcription	Hela-S3	cervix
12	chr16:30634800-30636000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:30635000-30636000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:30635200-30636000	Enhancers	Placenta	Placenta
15	chr16:30635200-30636000	Enhancers	HMEC	breast
16	chr16:30635200-30640000	Weak transcription	Liver	Liver
17	chr16:30635600-30635800	Bivalent/Poised TSS	HepG2	liver
18	chr16:30635600-30636000	Enhancers	Duodenum Mucosa	Duodenum
19	chr16:30635600-30636000	Enhancers	NHEK	skin

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