Variant report

Variant	rs62390706
Chromosome Location	chr6:1995606-1995607
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	chr6:1993624..1996051-chr6:2001806..2003962,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-11	chr6:1995530-1995609	NONHSAT106574

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11242730	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11242734	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11242735	0.85[EUR][1000 genomes]
rs12055694	0.81[ASN][1000 genomes]
rs12530335	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12661847	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17134651	0.81[ASN][1000 genomes]
rs4580917	0.83[ASN][1000 genomes]
rs55635233	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62390709	0.81[EUR][1000 genomes]
rs62390733	0.87[EUR][1000 genomes]
rs6920883	0.87[EUR][1000 genomes]
rs6921994	0.80[EUR][1000 genomes]
rs6924265	0.83[EUR][1000 genomes]
rs6935616	0.84[EUR][1000 genomes]
rs6935760	0.87[EUR][1000 genomes]
rs7745086	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7749136	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7753375	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7759455	0.83[ASN][1000 genomes]
rs9378666	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378667	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9378668	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9378670	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9378671	0.87[EUR][1000 genomes]
rs9378672	0.87[EUR][1000 genomes]
rs9378676	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9391941	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9391943	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9391944	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9392348	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392352	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9392353	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9392354	0.87[EUR][1000 genomes]
rs9392356	0.83[ASN][1000 genomes]
rs9405539	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405540	0.84[ASN][1000 genomes]
rs9405541	0.84[ASN][1000 genomes]
rs9405542	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2763525	chr6:1994892-2006033	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1985000-2010200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:1987400-2003600	Weak transcription	Aorta	Aorta
3	chr6:1988400-2008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:1990200-2008600	Weak transcription	Pancreas	Pancrea
5	chr6:1990400-2010800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:1992800-1997800	Weak transcription	Gastric	stomach
7	chr6:1992800-2010200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:1993000-2021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:1993200-2005400	Weak transcription	HepG2	liver
10	chr6:1993200-2007200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:1993400-2000400	Weak transcription	Primary T cells from cord blood	blood
12	chr6:1993800-2001000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:1994400-1995800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:1995000-1996200	Weak transcription	GM12878-XiMat	blood
15	chr6:1995400-1996200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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