Variant report

Variant	rs2282738
Chromosome Location	chr1:209882015-209882016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209879551..209882258-chr1:209882693..209884984,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1000282	0.87[EUR][1000 genomes]
rs1000283	0.90[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs10157973	0.85[CEU][hapmap]
rs10863783	0.88[EUR][1000 genomes]
rs10863785	0.88[EUR][1000 genomes]
rs11119327	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs11119330	0.88[EUR][1000 genomes]
rs11119331	0.88[EUR][1000 genomes]
rs11119332	0.87[EUR][1000 genomes]
rs11119336	0.84[CEU][hapmap]
rs11119337	0.86[AMR][1000 genomes]
rs11485195	0.88[EUR][1000 genomes]
rs11487866	0.88[EUR][1000 genomes]
rs11487867	0.81[CEU][hapmap]
rs11808690	0.88[EUR][1000 genomes]
rs12034758	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12059226	0.90[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs12060420	0.88[EUR][1000 genomes]
rs12060922	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs12086634	0.88[EUR][1000 genomes]
rs12090931	0.88[EUR][1000 genomes]
rs12094117	0.90[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs12116437	0.88[EUR][1000 genomes]
rs12120361	0.90[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs12129718	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138452	0.88[EUR][1000 genomes]
rs1337531	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1415542	0.90[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1415544	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17389184	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs17389198	0.85[CEU][hapmap]
rs1999826	0.83[EUR][1000 genomes]
rs2064148	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2205985	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2236903	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272867	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs2282739	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282741	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884090	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765240	0.83[EUR][1000 genomes]
rs3766618	0.80[CEU][hapmap]
rs3766619	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs3817821	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4314885	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844891	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627670	0.85[CEU][hapmap];0.80[LWK][hapmap];0.94[TSI][hapmap]
rs6540549	0.90[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6540550	0.85[CEU][hapmap]
rs6540553	0.85[CEU][hapmap]
rs6665715	0.85[CEU][hapmap];0.94[TSI][hapmap]
rs6672256	0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs667681	0.88[EUR][1000 genomes]
rs6679099	0.88[EUR][1000 genomes]
rs6679405	0.85[CEU][hapmap]
rs6700223	0.90[AMR][1000 genomes]
rs6702301	0.85[CEU][hapmap]
rs6752	0.88[EUR][1000 genomes]
rs7532324	0.91[EUR][1000 genomes]
rs7539852	0.90[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs7548781	0.95[CEU][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7555978	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs909710	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs932335	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9430012	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9430014	0.88[EUR][1000 genomes]
rs9430015	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9430016	0.90[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9430017	0.85[CEU][hapmap]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2282738	C20orf173	trans	parietal	SCAN
rs2282738	LAMB3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209875200-209882400	Enhancers	Brain Substantia Nigra	brain
2	chr1:209877400-209882600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:209878600-209888200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:209878800-209893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:209880600-209883800	Genic enhancers	Liver	Liver
6	chr1:209880800-209882200	Enhancers	Brain Germinal Matrix	brain
7	chr1:209880800-209882400	Enhancers	Brain Hippocampus Middle	brain
8	chr1:209881000-209883200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:209881000-209885200	Weak transcription	HUVEC	blood vessel
10	chr1:209881200-209882800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:209881200-209886000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:209881400-209882600	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:209881400-209883000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:209881400-209883600	Weak transcription	NHEK	skin
15	chr1:209881400-209884600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:209881400-209887200	Weak transcription	HMEC	breast
17	chr1:209881800-209882200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:209881800-209883600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:209882000-209884600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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