Variant report

Variant	rs10516862
Chromosome Location	chr4:90997171-90997172
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10516857	0.88[EUR][1000 genomes]
rs10516858	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10516860	0.91[EUR][1000 genomes]
rs10516864	0.92[ASN][1000 genomes]
rs11732065	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11933698	0.81[EUR][1000 genomes]
rs11941275	0.80[EUR][1000 genomes]
rs12500465	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12639636	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12642395	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12642404	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12643741	0.85[EUR][1000 genomes]
rs12647171	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12647266	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12648872	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12649987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650363	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12651123	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13103611	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13104940	0.92[ASN][1000 genomes]
rs13106409	0.89[EUR][1000 genomes]
rs13107286	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13108338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113863	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13119778	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13120745	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13121853	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13124133	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13126339	0.85[EUR][1000 genomes]
rs13131070	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13131903	0.88[EUR][1000 genomes]
rs13132515	0.83[EUR][1000 genomes]
rs13132730	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13143093	0.81[EUR][1000 genomes]
rs13148977	0.88[EUR][1000 genomes]
rs13149395	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13150124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13151441	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1443796	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1443798	0.87[EUR][1000 genomes]
rs1562034	0.91[EUR][1000 genomes]
rs17204072	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17204198	0.92[ASN][1000 genomes]
rs17205805	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs17808648	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17808829	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1835521	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1982293	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2120372	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2120375	0.88[EUR][1000 genomes]
rs34001515	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34064092	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34243515	0.93[ASN][1000 genomes]
rs34343229	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34886505	0.94[EUR][1000 genomes]
rs35197902	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36047807	0.92[ASN][1000 genomes]
rs3822098	0.87[CEU][hapmap]
rs55663876	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55686873	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62312690	0.86[EUR][1000 genomes]
rs62312738	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62312743	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62313888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532212	0.90[EUR][1000 genomes]
rs6532213	0.89[EUR][1000 genomes]
rs6814978	0.91[EUR][1000 genomes]
rs6819755	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6830014	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6837222	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs723992	0.88[EUR][1000 genomes]
rs72659470	0.90[ASN][1000 genomes]
rs7438673	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7660182	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7661577	0.88[EUR][1000 genomes]
rs7672024	0.92[ASN][1000 genomes]
rs7677884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7677966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7685355	0.88[EUR][1000 genomes]
rs992612	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830006	chr4:90971656-91186340	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv879538	chr4:90993172-91080308	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90990800-90999800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:90994800-90998400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:90994800-90998600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:90995600-90997200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:90996000-90998600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:90996000-91002800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:90996000-91002800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:90996200-90998800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:90996200-90999800	Weak transcription	GM12878-XiMat	blood
10	chr4:90996800-90999600	Weak transcription	Monocytes-CD14+_RO01746	blood

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