Variant report

Variant	rs42963
Chromosome Location	chr5:57567443-57567444
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	chr5:57564755..57567505-chr5:57575304..57577726,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1035475	1.00[CEU][hapmap]
rs10472035	0.88[CEU][hapmap]
rs10472036	0.88[CEU][hapmap]
rs13159047	1.00[YRI][hapmap]
rs13168414	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1469090	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs151868	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs152010	1.00[YRI][hapmap]
rs154670	0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154671	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs154673	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17709103	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs181745	1.00[ASW][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1981838	1.00[ASW][hapmap];0.88[CEU][hapmap]
rs2052547	0.89[ASN][1000 genomes]
rs2081087	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2216679	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2434584	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245282	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs245285	1.00[ASW][hapmap];0.91[CHD][hapmap];1.00[YRI][hapmap]
rs245287	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs245295	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs245493	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs2910569	0.88[CEU][hapmap]
rs2910573	1.00[YRI][hapmap]
rs2910577	1.00[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2910592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910594	0.88[CEU][hapmap]
rs2910600	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2910601	1.00[ASW][hapmap];0.88[CEU][hapmap]
rs2910605	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2910611	0.88[CEU][hapmap]
rs2964173	0.89[JPT][hapmap]
rs2964184	0.88[CEU][hapmap]
rs2964193	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964195	0.92[ASN][1000 genomes]
rs2964200	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964205	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37484	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs37485	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs37486	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs37487	0.95[ASN][1000 genomes]
rs37488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37516	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37526	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37527	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37528	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37533	0.82[AFR][1000 genomes]
rs37536	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs40209	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40210	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs41384	1.00[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs989579	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2762520	chr5:57557770-57578659	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs42963	BEND6	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57562600-57568000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:57563200-57569000	Weak transcription	A549	lung
3	chr5:57567000-57569200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:57567000-57571600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:57567200-57568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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