Variant report

Variant	rs6462447
Chromosome Location	chr7:3939055-3939056
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3937855..3940563-chr7:3945183..3947294,2	MCF-7	breast:
2	chr7:3443032..3445719-chr7:3938528..3940389,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10085400	0.81[CHB][hapmap]
rs10085568	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1013880	0.83[EUR][1000 genomes]
rs10215004	0.87[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10215340	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10241703	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap]
rs10242459	0.81[CHB][hapmap]
rs10243770	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs10244636	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs10245389	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10246449	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs10249255	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10250659	0.82[CEU][hapmap]
rs10254099	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs10256741	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs10262942	0.82[CEU][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10267786	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10273444	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs10479833	0.81[CHB][hapmap]
rs10479834	0.81[CHB][hapmap]
rs10951322	0.81[CHB][hapmap]
rs10951336	0.81[CHB][hapmap]
rs10951368	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10951374	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11514766	0.88[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11971293	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11973380	0.80[ASN][1000 genomes]
rs11974190	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11974357	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11976915	0.81[CHB][hapmap]
rs11977993	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11980947	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11982345	0.81[CHB][hapmap]
rs11983563	0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.80[ASN][1000 genomes]
rs12112335	0.81[CHB][hapmap]
rs12531980	0.81[CHB][hapmap]
rs12532040	0.81[CHB][hapmap]
rs12532171	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12532903	0.81[CHB][hapmap]
rs12532912	0.84[CHD][hapmap]
rs12533946	0.85[CEU][hapmap];0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs12536445	0.81[CHB][hapmap]
rs12537696	0.81[CHB][hapmap]
rs12538997	0.81[CHB][hapmap]
rs12690803	0.89[CHD][hapmap]
rs12690804	0.80[CEU][hapmap]
rs12701219	0.81[CHB][hapmap]
rs12701221	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12701229	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs12701262	0.82[CEU][hapmap]
rs12701271	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12701272	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13221624	0.81[CHB][hapmap]
rs13236719	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs13245096	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs1476644	0.89[CHD][hapmap]
rs1548612	0.81[CHB][hapmap]
rs17261199	0.81[CHB][hapmap]
rs1962783	0.81[CHB][hapmap]
rs1962784	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs1962785	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.81[AMR][1000 genomes]
rs2007554	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs2057920	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2057921	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs2079376	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2079377	0.83[AMR][1000 genomes]
rs2079378	0.83[AMR][1000 genomes]
rs2341959	0.81[CHB][hapmap]
rs2880159	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs2880204	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs41873	0.81[CHB][hapmap]
rs4431501	0.81[CHB][hapmap]
rs6462361	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs6462401	0.82[CEU][hapmap]
rs6462407	0.81[CHB][hapmap]
rs6462411	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes]
rs6462412	0.80[AMR][1000 genomes]
rs6462413	0.81[CHB][hapmap]
rs6945778	0.81[CHB][hapmap]
rs6948552	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6952864	0.81[CHB][hapmap]
rs6953282	0.81[CHB][hapmap]
rs6953604	0.81[CHB][hapmap]
rs6953707	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6955650	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs6956020	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6956479	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap]
rs6957166	0.81[CHB][hapmap]
rs6958535	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs6959492	0.81[CHB][hapmap]
rs6959674	0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6959835	0.81[CHB][hapmap]
rs6961230	0.81[CHB][hapmap]
rs6961561	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs6962058	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6962389	0.95[CHD][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs6962750	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6966030	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6968948	0.80[AMR][1000 genomes]
rs6969052	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs6970116	0.86[CHB][hapmap]
rs6971639	0.83[AMR][1000 genomes]
rs6971803	0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs6971828	0.89[CHD][hapmap]
rs6971873	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6972806	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs6973944	0.81[CHB][hapmap]
rs6975313	0.81[CHB][hapmap]
rs6975723	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs6977305	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs6977844	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs6978964	0.81[CHB][hapmap]
rs6979937	0.81[CHB][hapmap]
rs6980085	0.81[CHB][hapmap]
rs7778705	0.81[CHB][hapmap]
rs7783415	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7786556	0.95[CHD][hapmap];0.83[TSI][hapmap]
rs7794504	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs7804166	0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7807003	0.81[CHB][hapmap]
rs7809616	0.81[EUR][1000 genomes]
rs874344	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs917168	0.81[CHB][hapmap]
rs917198	0.81[CHB][hapmap]
rs9655343	0.81[CHB][hapmap]
rs9886069	0.87[EUR][1000 genomes]
rs9886234	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9986911	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1019190	chr7:3896634-3943566	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv519403	chr7:3932922-3939055	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv518377	chr7:3939055-3978342	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
2	chr7:3906800-3949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:3923000-3940000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:3932600-3939200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:3932800-3939200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:3933000-3939200	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:3935000-3940200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:3935800-3939400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr7:3936800-3974200	Weak transcription	Aorta	Aorta
10	chr7:3937400-3940400	Weak transcription	Fetal Brain Male	brain
11	chr7:3937800-3939200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:3937800-3943400	Weak transcription	Psoas Muscle	Psoas
13	chr7:3938000-3939200	Weak transcription	Spleen	Spleen
14	chr7:3938200-3939200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:3938800-3939600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:3938800-3941000	Enhancers	Fetal Muscle Leg	muscle
17	chr7:3939000-3939400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:3939000-3939400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:3939000-3939600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:3939000-3939600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr7:3939000-3939600	Enhancers	HSMM	muscle

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