Variant report

Variant	rs11240962
Chromosome Location	chr5:107721366-107721367
allele	A/C
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	POLR2A	chr5:107720753-107721453	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:107715567-107721797	GM12891	blood:	n/a	n/a
3	POLR2A	chr5:107716862-107721767	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107720815..107723363-chr5:107732371..107733940,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FER-2	chr5:107717801-107724211	NONHSAT103120

Variant related genes	Relation type
FBXL17	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10035966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10040007	1.00[CHB][hapmap]
rs10045002	1.00[CHB][hapmap]
rs10045508	0.92[EUR][1000 genomes]
rs10054662	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10057896	1.00[CHB][hapmap]
rs10061049	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10070927	1.00[CHB][hapmap]
rs10071499	1.00[CHB][hapmap]
rs10075370	1.00[CHB][hapmap]
rs10078397	0.92[EUR][1000 genomes]
rs10463587	0.92[EUR][1000 genomes]
rs10477896	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11742268	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948261	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11949077	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11949079	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12187433	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13361152	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1510967	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171756	1.00[CHB][hapmap]
rs17388874	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17454114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076794	1.00[CHB][hapmap]
rs2112303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs28572757	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28752150	0.92[ASN][1000 genomes]
rs2910791	1.00[CHB][hapmap]
rs2922408	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2922425	1.00[CHB][hapmap]
rs2922431	1.00[CHB][hapmap]
rs2966788	1.00[CHB][hapmap]
rs2966800	1.00[CHB][hapmap]
rs2966803	1.00[CHB][hapmap]
rs2966820	1.00[CHB][hapmap]
rs2966821	1.00[CHB][hapmap]
rs2966823	1.00[CHB][hapmap]
rs2966825	1.00[CHB][hapmap]
rs2966829	1.00[CHB][hapmap]
rs2966833	1.00[CHB][hapmap]
rs4413518	0.89[EUR][1000 genomes]
rs4957551	1.00[CHB][hapmap]
rs57370105	0.84[ASN][1000 genomes]
rs59423465	0.90[EUR][1000 genomes]
rs60045633	0.91[EUR][1000 genomes]
rs60896544	0.90[EUR][1000 genomes]
rs62362279	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62362281	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362302	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594295	1.00[CHB][hapmap]
rs6863456	1.00[CHB][hapmap]
rs6869057	1.00[CHB][hapmap]
rs6876738	0.88[EUR][1000 genomes]
rs6880727	1.00[CHB][hapmap]
rs6881232	0.90[EUR][1000 genomes]
rs6881879	1.00[CHB][hapmap]
rs6885988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6895295	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7706429	1.00[CHB][hapmap]
rs7714342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7720469	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7720841	0.91[EUR][1000 genomes]
rs7727051	1.00[CHB][hapmap]
rs7733311	1.00[CHB][hapmap]
rs9326727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107718800-107731200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:107719000-107722000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:107719000-107722200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:107719000-107722200	Weak transcription	NHDF-Ad	bronchial
5	chr5:107719000-107722200	Weak transcription	Osteobl	bone
6	chr5:107719000-107723800	Weak transcription	Fetal Brain Female	brain
7	chr5:107719200-107722800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:107719400-107721800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:107719400-107723400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:107719800-107721600	Weak transcription	HepG2	liver
11	chr5:107721000-107722200	Weak transcription	HSMM	muscle

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