Variant report

Variant	rs3789112
Chromosome Location	chr2:111714577-111714578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111706009..111708285-chr2:111713250..111715688,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10164695	0.89[JPT][hapmap]
rs10165663	0.85[JPT][hapmap]
rs10169926	0.84[JPT][hapmap]
rs10171765	0.81[JPT][hapmap]
rs10175204	0.85[JPT][hapmap]
rs10177582	0.84[JPT][hapmap]
rs10185326	0.84[JPT][hapmap]
rs10186753	0.85[JPT][hapmap]
rs10197135	0.85[JPT][hapmap]
rs10202539	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10204997	0.85[JPT][hapmap]
rs10208020	0.88[JPT][hapmap]
rs11123221	0.84[JPT][hapmap]
rs11123229	0.85[JPT][hapmap]
rs1114413	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1114414	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12328918	0.85[JPT][hapmap]
rs12470827	0.85[JPT][hapmap]
rs12476386	0.85[JPT][hapmap]
rs13024140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13384044	0.84[JPT][hapmap]
rs13413838	0.89[ASN][1000 genomes]
rs13424637	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13429695	0.89[JPT][hapmap]
rs1513826	0.84[JPT][hapmap]
rs17466576	0.84[JPT][hapmap]
rs1872062	0.84[JPT][hapmap]
rs2128815	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341913	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789114	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789116	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789121	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789127	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3827548	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848344	0.89[ASN][1000 genomes]
rs4849164	0.84[JPT][hapmap]
rs4849165	0.84[JPT][hapmap]
rs4849170	0.85[JPT][hapmap]
rs4849298	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62159558	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6542188	0.84[JPT][hapmap]
rs6542189	0.84[JPT][hapmap]
rs6542190	0.84[JPT][hapmap]
rs6720034	0.84[JPT][hapmap]
rs6751930	0.83[JPT][hapmap]
rs7355443	0.85[JPT][hapmap]
rs7355554	0.85[JPT][hapmap]
rs7569806	0.85[JPT][hapmap]
rs9308692	0.84[JPT][hapmap]
rs932076	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1004949	chr2:111607532-111780719	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1002568	chr2:111607532-111781442	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1005665	chr2:111610107-111762039	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535892	chr2:111610107-111762039	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111707000-111729600	Weak transcription	Right Atrium	heart
2	chr2:111712800-111716200	Weak transcription	Fetal Intestine Large	intestine
3	chr2:111713000-111723000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:111713200-111716400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:111713200-111723400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:111713200-111725200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:111713400-111729800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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