Variant report

Variant	rs2056925
Chromosome Location	chr6:27690905-27690906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27684698..27689044-chr6:27689656..27693289,4	K562	blood:
2	chr6:27690338..27692656-chr6:27698623..27701642,3	K562	blood:
3	chr6:27687897..27691780-chr6:27691811..27694513,3	MCF-7	breast:
4	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10214440	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10484401	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1139226	0.85[ASN][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13215072	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1985099	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200468	0.84[ASN][1000 genomes]
rs200476	0.81[ASN][1000 genomes]
rs200502	0.86[CEU][hapmap]
rs2092075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2179095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2394000	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394002	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2893929	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2893931	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34752872	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35069907	0.81[EUR][1000 genomes]
rs35957409	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711163	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713118	0.84[ASN][1000 genomes]
rs4713121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6901520	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914924	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922574	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs742046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7756968	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7759217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7760523	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7772027	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7776351	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9283880	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283881	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283882	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283883	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295740	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9295742	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295743	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9348774	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9348775	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357045	0.94[ASN][1000 genomes]
rs9366700	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366702	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368528	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368529	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368530	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380010	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380011	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380012	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393847	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393848	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461401	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461405	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468195	0.84[ASN][1000 genomes]
rs9468199	0.87[ASN][1000 genomes]
rs9468200	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468201	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468203	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468204	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468206	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468217	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468219	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468220	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3327708	chr6:27683503-27692934	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2056925	BTN3A3	cis	cerebellum	SCAN
rs2056925	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2056925	OR2B8P	cis	Thyroid	GTEx
rs2056925	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2056925	ZKSCAN3	cis	parietal	SCAN
rs2056925	AL022393.7	cis	Muscle Skeletal	GTEx
rs2056925	BTN2A1	cis	parietal	SCAN
rs2056925	BTN3A3	cis	parietal	SCAN
rs2056925	ZNF204P	cis	parietal	SCAN
rs2056925	HIST1H3D	cis	parietal	SCAN
rs2056925	HIST1H2BM	cis	cerebellum	SCAN
rs2056925	BTN2A2	Cis_chr	lymphoblastoid	RTeQTL
rs2056925	HIST1H3C	cis	cerebellum	SCAN
rs2056925	RP1-265C24.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:27689600-27691600	Weak transcription	NHEK	skin
3	chr6:27689600-27694200	Weak transcription	A549	lung
4	chr6:27690200-27691600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27690200-27691600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:27690200-27694400	Weak transcription	K562	blood

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