Variant report

Variant	rs12599861
Chromosome Location	chr16:72328626-72328627
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	chr16:72314956..72316572-chr16:72326957..72329841,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10492815	1.00[AFR][1000 genomes]
rs11075930	1.00[AFR][1000 genomes]
rs11531326	1.00[AFR][1000 genomes]
rs12051317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12595984	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12596421	1.00[AFR][1000 genomes]
rs12596520	1.00[AFR][1000 genomes]
rs12596827	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12597916	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12598100	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12600175	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12600298	0.83[AFR][1000 genomes]
rs1437196	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16970845	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16970852	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs16970879	1.00[AFR][1000 genomes]
rs16970888	1.00[AFR][1000 genomes]
rs16970895	1.00[AFR][1000 genomes]
rs16970901	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16970906	1.00[AFR][1000 genomes]
rs16970922	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16970998	1.00[AFR][1000 genomes]
rs2059901	0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2161659	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2878752	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28823672	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28876074	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788468	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4788627	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788629	1.00[AFR][1000 genomes]
rs4788633	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4788634	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4788637	0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58097957	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60144415	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs873899	1.00[AFR][1000 genomes]
rs9938153	0.81[ASN][1000 genomes]
rs9989361	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72302600-72332000	Weak transcription	Primary B cells from cord blood	blood
2	chr16:72315600-72353600	Weak transcription	Dnd41	blood
3	chr16:72316600-72334800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:72317400-72331800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:72318600-72329200	Weak transcription	HepG2	liver
6	chr16:72325400-72342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:72326200-72334800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr16:72327200-72330000	Weak transcription	NHEK	skin
9	chr16:72327200-72332200	Weak transcription	Hela-S3	cervix

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