Variant report

Variant	rs8046001
Chromosome Location	chr16:30833321-30833322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:30825905..30827673-chr16:30830413..30833381,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11150596	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11150599	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11864054	0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs12447534	0.87[EUR][1000 genomes]
rs12926237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926295	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs13337900	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13338946	0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs2289442	0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs28421305	1.00[ASN][1000 genomes]
rs35629860	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3747481	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs3747486	0.81[ASW][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap]
rs3812999	0.81[ASW][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap]
rs4889489	0.89[EUR][1000 genomes]
rs4889490	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4889614	0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4889627	0.81[ASN][1000 genomes]
rs4889630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4889651	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4889653	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs62057223	0.87[EUR][1000 genomes]
rs6565207	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7186852	0.88[CHD][hapmap]
rs7187359	0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs7192475	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7197475	0.88[CHD][hapmap]
rs7198250	0.81[ASW][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap]
rs72799316	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73524556	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7500719	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8046391	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8050330	0.95[EUR][1000 genomes]
rs8058578	0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs8058961	0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs8063565	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs885107	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9319587	1.00[ASN][1000 genomes]
rs9925025	0.88[CHD][hapmap]
rs9932572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9933843	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs9933875	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9934249	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938088	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9939243	0.81[EUR][1000 genomes]

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	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	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
4	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
5	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
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
11	nsv905732	chr16:30788182-30837210	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic 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	40 gene(s)	inside rSNPs	diseases
12	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
13	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
14	nsv1060384	chr16:30802415-30878838	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1059633	chr16:30803099-30867916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8046001	BCL7C	cis	cerebellum	SCAN
rs8046001	ITGAX	cis	parietal	SCAN
rs8046001	RABEP2	cis	cerebellum	SCAN
rs8046001	MYST1	cis	parietal	SCAN
rs8046001	MYST1	cis	cerebellum	SCAN
rs8046001	PHKG2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30826400-30844800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:30826600-30835200	Weak transcription	Gastric	stomach
3	chr16:30826600-30835200	Weak transcription	Stomach Mucosa	stomach
4	chr16:30831800-30833400	Weak transcription	Brain Angular Gyrus	brain
5	chr16:30832400-30844600	Weak transcription	Ovary	ovary
6	chr16:30832600-30833400	Flanking Active TSS	HepG2	liver
7	chr16:30832600-30833600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr16:30832600-30835200	Weak transcription	Esophagus	oesophagus
9	chr16:30833000-30835000	Weak transcription	A549	lung
10	chr16:30833200-30833400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:30833200-30833400	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr16:30833200-30833600	Enhancers	Sigmoid Colon	Sigmoid Colon

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