Variant report

Variant	rs9399287
Chromosome Location	chr6:139958154-139958155
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139957877..139959819-chr6:139968952..139970671,2	K562	blood:
2	chr6:139694107..139696475-chr6:139956722..139958625,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10223884	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12202000	0.84[EUR][1000 genomes]
rs12203872	0.82[EUR][1000 genomes]
rs12211407	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1541249	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1936211	0.97[AFR][1000 genomes]
rs2327975	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2327976	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2876419	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4317424	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4419683	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4419684	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4895574	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896478	0.83[EUR][1000 genomes]
rs4896479	0.83[EUR][1000 genomes]
rs4896480	0.83[EUR][1000 genomes]
rs4896483	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6570368	0.98[AFR][1000 genomes]
rs6917245	0.98[AFR][1000 genomes]
rs6917394	0.99[AFR][1000 genomes]
rs6917655	0.98[AFR][1000 genomes]
rs6940157	0.99[AFR][1000 genomes]
rs7383441	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7738637	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7738952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7759402	0.98[AFR][1000 genomes]
rs9285491	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9321734	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9321735	0.84[EUR][1000 genomes]
rs9321737	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9321738	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321739	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373239	0.80[EUR][1000 genomes]
rs9373240	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376438	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9376441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389700	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9389702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403095	0.84[EUR][1000 genomes]
rs9484293	0.83[EUR][1000 genomes]
rs9484294	0.83[EUR][1000 genomes]
rs9484298	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9495552	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 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	chr6:139949800-139959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:139955200-139958400	Weak transcription	K562	blood
3	chr6:139956600-139958600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:139956800-139959000	Enhancers	Placenta	Placenta
5	chr6:139957200-139976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:139957800-139960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:139958000-139959000	Enhancers	Cortex derived primary cultured neurospheres	brain

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