Variant report

Variant	rs7531411
Chromosome Location	chr1:77796413-77796414
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	chr1:77786657..77790465-chr1:77794165..77797983,5	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10747354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1167202	0.96[YRI][hapmap]
rs1167207	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1167212	0.81[ASW][hapmap];0.96[YRI][hapmap]
rs1167215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1167217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177502	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1377733	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1377734	0.89[ASN][1000 genomes]
rs1463324	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851736	0.86[CEU][hapmap]
rs2602929	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602934	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602943	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602945	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602946	0.86[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602948	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602951	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689676	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2689683	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799550	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799554	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799555	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799556	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799558	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799559	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799560	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799561	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799562	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2799563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815309	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815310	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815311	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815312	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2815314	0.86[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815317	0.88[CEU][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815319	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815327	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815337	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662853	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936001	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9439799	0.81[ASW][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9439819	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7531411	LRRIQ3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77785200-77799200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:77788600-77798600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:77788600-77805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:77788800-77813000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:77789000-77813000	Weak transcription	NHLF	lung
6	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:77789600-77798600	Weak transcription	A549	lung
8	chr1:77789800-77800600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:77790000-77798600	Weak transcription	NHDF-Ad	bronchial
10	chr1:77790000-77808600	Weak transcription	HSMM	muscle
11	chr1:77790400-77804200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:77790600-77805800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:77790600-77808600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:77795400-77799600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:77795600-77799200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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