Variant report

Variant	rs6460539
Chromosome Location	chr7:69626246-69626247
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	chr7:69507240..69508178-chr7:69626181..69627189,3	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10499813	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12112758	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12113555	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12155144	0.84[EUR][1000 genomes]
rs12667561	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12669794	0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12673575	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698826	0.87[ASN][1000 genomes]
rs12698835	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12698838	0.85[AFR][1000 genomes]
rs12698841	0.86[AFR][1000 genomes]
rs12698843	0.84[AFR][1000 genomes]
rs12698846	0.92[AFR][1000 genomes]
rs12698847	0.92[AFR][1000 genomes]
rs12698850	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12698851	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12698853	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12698856	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12698857	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12698859	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12698861	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12698862	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698864	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698865	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698867	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698869	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698873	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698875	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12698879	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698880	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698882	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698883	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698884	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698886	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12698892	0.84[EUR][1000 genomes]
rs13229395	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13229686	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13231497	0.85[AFR][1000 genomes]
rs13238017	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13242485	0.86[AFR][1000 genomes]
rs13340492	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357759	0.81[JPT][hapmap]
rs1404275	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476104	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1476105	0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17365333	0.90[AFR][1000 genomes]
rs17365375	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17462837	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17604001	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17762460	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880369	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2030705	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030706	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866275	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34519726	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35062112	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35317642	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4318956	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4475377	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4623296	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58849135	0.90[AFR][1000 genomes]
rs66936223	0.85[EUR][1000 genomes]
rs67847242	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943630	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6945241	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946066	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6948676	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6951909	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6953075	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6964139	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6970670	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6971237	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6975814	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978919	0.84[EUR][1000 genomes]
rs735060	0.82[AFR][1000 genomes]
rs7779308	0.86[AFR][1000 genomes]
rs7780640	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7782771	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7783039	0.80[AFR][1000 genomes]
rs7783592	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783748	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790084	0.96[AFR][1000 genomes]
rs7791954	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7799192	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7800317	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7800759	0.85[AFR][1000 genomes]
rs7803814	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7806363	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7807263	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7808588	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs870919	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs877188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs917717	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9647931	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9647932	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9691023	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][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	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018289	chr7:69383450-69650885	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538922	chr7:69383450-69650885	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1020488	chr7:69465268-69671126	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69600000-69631000	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69610200-69626400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr7:69620200-69628400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:69621600-69626400	Weak transcription	HSMM	muscle
5	chr7:69621600-69628400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:69624600-69628400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:69625400-69627000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:69625600-69626600	Enhancers	Fetal Brain Male	brain
9	chr7:69625600-69626800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr7:69625600-69626800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:69625800-69626600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:69625800-69626800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr7:69625800-69626800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr7:69625800-69626800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:69625800-69626800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr7:69626000-69626600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr7:69626000-69626800	Enhancers	HUES6 Cell Line	embryonic stem cell

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