Variant report

Variant	rs878943
Chromosome Location	chr13:54697600-54697601
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:54693602..54695448-chr13:54696284..54698888,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10467530	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1334874	0.96[EUR][1000 genomes]
rs1335976	0.95[EUR][1000 genomes]
rs1335977	0.95[EUR][1000 genomes]
rs1335979	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335980	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1577576	0.97[EUR][1000 genomes]
rs1763779	0.86[EUR][1000 genomes]
rs1932503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984140	0.86[AMR][1000 genomes]
rs1984141	0.86[AMR][1000 genomes]
rs2005372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050536	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210849	0.89[EUR][1000 genomes]
rs2260462	0.87[ASN][1000 genomes]
rs2261357	0.86[JPT][hapmap]
rs2261359	0.86[JPT][hapmap]
rs2261365	0.86[JPT][hapmap]
rs2408992	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2408993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576118	0.85[ASN][1000 genomes]
rs2576125	0.88[AMR][1000 genomes]
rs2576126	0.86[AMR][1000 genomes]
rs2576127	0.86[AMR][1000 genomes]
rs2576128	0.88[AMR][1000 genomes]
rs2576129	0.88[AMR][1000 genomes]
rs2576131	0.86[AMR][1000 genomes]
rs2576132	0.88[ASN][1000 genomes]
rs2576135	0.86[AMR][1000 genomes]
rs2576143	0.85[ASN][1000 genomes]
rs2576144	0.85[ASN][1000 genomes]
rs2784552	0.86[JPT][hapmap]
rs2784555	0.81[AMR][1000 genomes]
rs2784558	0.88[ASN][1000 genomes]
rs2784559	0.88[AMR][1000 genomes]
rs2784560	0.88[AMR][1000 genomes]
rs2784561	0.86[AMR][1000 genomes]
rs2784562	0.86[AMR][1000 genomes]
rs2784564	0.88[AMR][1000 genomes]
rs4274311	0.97[EUR][1000 genomes]
rs4883848	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4884867	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510147	0.86[EUR][1000 genomes]
rs551408	0.95[EUR][1000 genomes]
rs564930	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs574623	0.95[EUR][1000 genomes]
rs600930	0.95[EUR][1000 genomes]
rs61956190	0.97[EUR][1000 genomes]
rs653228	0.95[EUR][1000 genomes]
rs6561766	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6561768	0.95[EUR][1000 genomes]
rs657383	0.86[EUR][1000 genomes]
rs667408	0.95[EUR][1000 genomes]
rs681704	0.95[EUR][1000 genomes]
rs7326186	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7326388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7329766	0.93[EUR][1000 genomes]
rs7335075	0.95[EUR][1000 genomes]
rs7335475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795642	0.81[ASN][1000 genomes]
rs795643	0.81[ASN][1000 genomes]
rs7984593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985834	0.99[EUR][1000 genomes]
rs7986212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992992	0.97[EUR][1000 genomes]
rs8001182	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878942	0.86[AMR][1000 genomes]
rs9527179	0.97[EUR][1000 genomes]
rs9536639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568990	0.97[EUR][1000 genomes]
rs9596914	0.84[EUR][1000 genomes]
rs988526	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988527	0.86[AMR][1000 genomes]
rs988528	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1049	chr13:54684354-54728981	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757533	chr13:54692032-54711236	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2759938	chr13:54692032-54711236	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54683200-54698800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:54688600-54699000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:54689000-54706000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:54689400-54700000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr13:54691800-54706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:54692600-54705000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr13:54693800-54700000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:54695800-54697600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:54696200-54700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:54696400-54699200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr13:54697200-54700600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:54697600-54702600	Strong transcription	H9 Cell Line	embryonic stem cell

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