Variant report

Variant	rs2142093
Chromosome Location	chr8:91095517-91095518
allele	C/T
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	REST	chr8:91094104-91095737	MCF-7	breast:	n/a	n/a
2	REST	chr8:91094624-91095622	PANC-1	pancreas:	n/a	n/a
3	SIN3AK20	chr8:91094571-91095560	MCF-7	breast:	n/a	n/a
4	REST	chr8:91094571-91095554	ECC-1	luminal epithelium:	n/a	n/a
5	REST	chr8:91094184-91095548	PFSK-1	brain:	n/a	n/a
6	REST	chr8:91094461-91095629	ECC-1	luminal epithelium:	n/a	n/a
7	GATA3	chr8:91095408-91095656	SH-SY5Y	brain:	n/a	chr8:91095432-91095443
8	MXI1	chr8:91094250-91095632	SK-N-SH	brain:	n/a	n/a
9	REST	chr8:91094027-91095672	HL-60	blood:	n/a	n/a
10	REST	chr8:91094639-91095800	PANC-1	pancreas:	n/a	n/a
11	REST	chr8:91094333-91095535	MCF-7	breast:	n/a	n/a
12	REST	chr8:91094118-91095620	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:91085654..91087463-chr8:91095150..91097801,2	K562	blood:

Variant related genes	Relation type
CALB1	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10088137	0.86[CEU][hapmap]
rs10092098	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs10095826	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10100369	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs10104321	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1011682	0.91[CEU][hapmap];0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs1011683	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs1061302	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1063045	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs10755930	0.84[EUR][1000 genomes]
rs10956375	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs11782032	0.90[CEU][hapmap]
rs12171665	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12547667	0.82[EUR][1000 genomes]
rs12549107	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs12679577	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs13265193	0.81[CEU][hapmap]
rs13275276	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs13277204	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13278453	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs13312935	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs1554927	0.80[EUR][1000 genomes]
rs1800645	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1805790	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs1805794	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1805795	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs1805797	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1805799	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1805800	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs1805808	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs1805818	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1805844	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs1805870	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1805871	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1805874	0.86[CEU][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs1805876	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1805877	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2063976	0.86[EUR][1000 genomes]
rs2073635	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs2074593	0.80[EUR][1000 genomes]
rs2074596	0.80[CEU][hapmap]
rs2091887	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2091900	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2097825	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2107465	0.80[CEU][hapmap]
rs2142094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205108	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2234744	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2267543	0.80[CEU][hapmap]
rs2280780	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs2308962	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2339025	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs28380191	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3087750	0.86[EUR][1000 genomes]
rs34915823	0.86[EUR][1000 genomes]
rs35044745	0.87[EUR][1000 genomes]
rs3736639	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs3758146	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs4961166	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs6470523	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs6470524	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs6470668	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6470671	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6470708	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6470709	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6470713	0.90[CEU][hapmap]
rs6985793	0.85[CEU][hapmap]
rs6987873	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs6988013	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6990969	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs6991811	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs6993054	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs6994202	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7006322	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs7011299	0.91[CEU][hapmap];0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs7012846	0.81[CEU][hapmap]
rs7018118	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs71528739	0.82[EUR][1000 genomes]
rs741777	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs741778	0.81[CEU][hapmap]
rs7459441	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7459577	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7459845	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7459846	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7461859	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7463278	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs7463923	0.81[EUR][1000 genomes]
rs7465539	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7815279	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7816839	0.80[CEU][hapmap]
rs7821408	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7822272	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs7822950	0.80[EUR][1000 genomes]
rs7829246	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs7831184	0.80[EUR][1000 genomes]
rs926092	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs9649958	0.81[CEU][hapmap]
rs9774207	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9792335	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs988934	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891183	chr8:90975550-91111193	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
2	esv2758164	chr8:91000786-91329669	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2759628	chr8:91000786-91329669	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv2757281	chr8:91090821-91235335	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2142093	NBN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91095000-91095600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr8:91095200-91098400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr8:91095200-91098400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:91095200-91098800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr8:91095200-91099200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:91095400-91095600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:91095400-91095600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:91095400-91095600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:91095400-91095600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:91095400-91095600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr8:91095400-91095600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr8:91095400-91095600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:91095400-91095800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr8:91095400-91095800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:91095400-91096000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr8:91095400-91098200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr8:91095400-91098600	Weak transcription	H9 Cell Line	embryonic stem cell

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