Variant report

Variant	rs2300168
Chromosome Location	chr1:71473791-71473792
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	GATA3	chr1:71473605-71473835	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71473756..71476164-chr1:71480981..71482752,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZRANB2-2	chr1:71472542-71473814	NONHSAT003875

Variant related genes	Relation type
ENSG00000269933	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11209732	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209742	0.86[ASN][1000 genomes]
rs12035634	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12039343	0.81[EUR][1000 genomes]
rs12405786	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409164	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17090778	0.81[AMR][1000 genomes]
rs1883460	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2206343	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2223501	0.81[ASN][1000 genomes]
rs2256385	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2268052	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2284361	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2284363	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300162	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2300165	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2300176	0.99[ASN][1000 genomes]
rs2300177	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35316490	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3819787	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4649933	0.99[ASN][1000 genomes]
rs484538	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs5024204	0.92[ASN][1000 genomes]
rs55669216	0.81[EUR][1000 genomes]
rs5675	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570021	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6424414	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs646511	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs646621	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs66539808	0.90[ASN][1000 genomes]
rs6678886	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66904764	0.90[ASN][1000 genomes]
rs6698339	0.82[EUR][1000 genomes]
rs7531139	0.92[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7534885	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909848	0.81[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830148	chr1:71310366-71483932	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv871313	chr1:71391646-71489438	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008902	chr1:71417926-71488139	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv534989	chr1:71417926-71488139	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv871222	chr1:71427842-71473791	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
8	nsv461851	chr1:71442626-71507541	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv546473	chr1:71442626-71507541	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
10	esv1850593	chr1:71444149-71514969	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv870843	chr1:71465292-71489438	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
12	nsv870734	chr1:71469583-71485036	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	nsv870576	chr1:71469583-71489438	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71465800-71485000	Weak transcription	Pancreas	Pancrea
2	chr1:71466000-71475200	Weak transcription	K562	blood
3	chr1:71467800-71475400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:71470600-71477600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:71472800-71474000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:71473600-71478000	Weak transcription	Aorta	Aorta

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