Variant report

Variant	rs1415542
Chromosome Location	chr1:209902110-209902111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209901662-209902708	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209901763..209904735-chr1:209904804..209907749,3	K562	blood:
2	chr1:209900061..209902674-chr1:209907942..209909580,2	K562	blood:

Variant related genes	Relation type
ENSG00000227591	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

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];0.94[MEX][hapmap];1.00[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	0.99[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];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[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];1.00[MEX][hapmap]
rs11119341	0.93[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	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[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	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060420	0.80[AFR][1000 genomes];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];0.80[AFR][1000 genomes];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	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[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	0.85[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129718	0.95[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]
rs1415544	0.90[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]
rs17015169	0.82[MEX][hapmap]
rs17389184	0.90[CEU][hapmap];0.93[MEX][hapmap];0.90[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];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282738	0.90[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2282739	0.95[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2282741	0.90[EUR][1000 genomes]
rs2884090	0.90[EUR][1000 genomes]
rs3753606	0.82[MEX][hapmap]
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];0.94[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];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6540549	0.90[CEU][hapmap];0.88[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];0.82[MEX][hapmap]
rs6665715	0.95[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs6672256	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[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	0.80[AFR][1000 genomes];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	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7539852	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]
rs7548781	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7555978	0.87[EUR][1000 genomes]
rs909710	0.95[CEU][hapmap];1.00[MEX][hapmap];0.93[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];1.00[YRI][hapmap];0.99[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];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430014	0.94[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[CHD][hapmap];0.88[MEX][hapmap];0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1415542	IRF6	cis	cerebellum	SCAN
rs1415542	TRAF3IP3	cis	Whole Blood	GTEx
rs1415542	HSD11B1	cis	cerebellum	SCAN
rs1415542	SYT14	cis	parietal	SCAN
rs1415542	SRGAP2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209894400-209907400	Weak transcription	Right Ventricle	heart
2	chr1:209895200-209902400	Weak transcription	Left Ventricle	heart
3	chr1:209897600-209903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209897800-209906200	Weak transcription	Ovary	ovary
5	chr1:209898000-209902200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:209899600-209902400	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:209900200-209902600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:209900400-209902400	Enhancers	Brain Substantia Nigra	brain
9	chr1:209900800-209902400	Enhancers	Brain Anterior Caudate	brain
10	chr1:209901000-209902200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:209901000-209903000	Enhancers	Fetal Heart	heart
12	chr1:209901200-209906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:209901800-209902400	Enhancers	Brain Angular Gyrus	brain
14	chr1:209902000-209905000	Weak transcription	Liver	Liver

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