Variant report

Variant	rs6989402
Chromosome Location	chr8:89390946-89390947
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	chr8:89389126..89391030-chr8:89391049..89394104,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10100170	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012116	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10504840	0.83[ASN][1000 genomes]
rs10504845	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1094195	0.83[ASN][1000 genomes]
rs1094196	0.83[ASN][1000 genomes]
rs1094198	0.83[ASN][1000 genomes]
rs11774961	0.90[ASN][1000 genomes]
rs13250349	0.91[ASN][1000 genomes]
rs13258321	0.83[ASN][1000 genomes]
rs13261175	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262875	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13271448	0.83[ASN][1000 genomes]
rs13279451	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1394511	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504798	0.83[ASN][1000 genomes]
rs1504799	0.83[ASN][1000 genomes]
rs1504801	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881203	0.90[EUR][1000 genomes]
rs16881281	0.81[CEU][hapmap]
rs16882957	0.83[ASN][1000 genomes]
rs16892543	0.90[EUR][1000 genomes]
rs1825876	0.83[ASN][1000 genomes]
rs1910730	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28787399	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34051963	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34583542	0.83[ASN][1000 genomes]
rs35175011	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35660410	0.92[ASN][1000 genomes]
rs4246109	0.90[EUR][1000 genomes]
rs4246111	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4369037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4395935	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461943	1.00[ASN][1000 genomes]
rs4497011	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4604492	0.90[ASN][1000 genomes]
rs4961095	0.92[ASN][1000 genomes]
rs56231945	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58255283	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58418586	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58644813	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469364	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469372	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67312178	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984041	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6992417	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6994283	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7003288	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7003388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7003595	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7004601	1.00[ASN][1000 genomes]
rs7006944	1.00[ASN][1000 genomes]
rs73291155	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7820710	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7823223	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825672	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821112	0.83[ASN][1000 genomes]
rs821113	0.83[ASN][1000 genomes]
rs821115	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831386	chr8:89209788-89403546	Enhancers Genic enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv891171	chr8:89342944-89439469	Enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6989402	ARHGEF16	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89380600-89394800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:89389400-89392800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:89390400-89391200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr8:89390800-89391400	Enhancers	Pancreatic Islets	Pancreatic Islet

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