Variant report

Variant	rs7539852
Chromosome Location	chr1:209898539-209898540
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	chr1:209897489..209898995-chr1:209918699..209920810,2	K562	blood:
2	chr1:209898273..209898882-chr1:209921133..209921700,3	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1000282	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1000283	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1007693	0.81[CEU][hapmap]
rs10157973	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10863783	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863785	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119327	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119328	0.86[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119330	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119331	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119332	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119336	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11119340	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs11119341	1.00[MEX][hapmap]
rs11485195	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11487866	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11487867	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806703	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11807619	0.85[ASW][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11808690	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11811440	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12030655	0.86[EUR][1000 genomes]
rs12034758	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12059226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060420	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12060922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086634	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12090931	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12094117	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12116437	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120361	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129718	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12138452	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1337531	0.90[EUR][1000 genomes]
rs1415542	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415544	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1474654	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474655	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389184	0.90[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs17389198	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1999826	0.92[EUR][1000 genomes]
rs2064148	0.90[EUR][1000 genomes]
rs2205985	0.89[EUR][1000 genomes]
rs2236903	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs2272867	0.95[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282738	0.90[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2282739	0.95[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2282741	0.90[EUR][1000 genomes]
rs2884090	0.90[EUR][1000 genomes]
rs3765240	0.92[EUR][1000 genomes]
rs3766618	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3766619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817821	0.84[EUR][1000 genomes]
rs4314885	0.89[EUR][1000 genomes]
rs4844891	0.95[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs61820570	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627670	0.95[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs6540549	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs6540550	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6540551	0.87[EUR][1000 genomes]
rs6540552	0.85[EUR][1000 genomes]
rs6540553	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6540554	0.81[CEU][hapmap]
rs6665715	0.95[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs6672256	0.85[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667681	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679099	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679405	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6702301	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6752	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs679846	0.83[EUR][1000 genomes]
rs7521461	0.85[EUR][1000 genomes]
rs7532324	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7548781	0.95[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7555978	0.87[EUR][1000 genomes]
rs909710	0.95[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs932335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430014	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430015	0.90[EUR][1000 genomes]
rs9430016	1.00[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9430017	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][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	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
5	nsv525445	chr1:209885318-209912593	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7539852	IRF6	cis	cerebellum	SCAN
rs7539852	TRAF3IP3	cis	Whole Blood	GTEx
rs7539852	HSD11B1	cis	cerebellum	SCAN
rs7539852	SRGAP2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209893600-209899000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:209894400-209907400	Weak transcription	Right Ventricle	heart
3	chr1:209894600-209899800	Weak transcription	Fetal Heart	heart
4	chr1:209895200-209902400	Weak transcription	Left Ventricle	heart
5	chr1:209896800-209898600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:209896800-209899200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:209897000-209898600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:209897000-209898800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:209897000-209899000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:209897200-209898800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:209897600-209899800	Enhancers	Liver	Liver
12	chr1:209897600-209903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209897800-209906200	Weak transcription	Ovary	ovary
14	chr1:209898000-209898600	Enhancers	Primary T cells from cord blood	blood
15	chr1:209898000-209900200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:209898000-209902200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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