Variant report

Variant	rs186376
Chromosome Location	chr1:86286459-86286460
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86283944..86286909-chr1:86290122..86291813,2	MCF-7	breast:
2	chr1:86211855..86213533-chr1:86285001..86287776,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1072508	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1072509	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10873730	1.00[CHB][hapmap]
rs10873731	0.86[CHB][hapmap]
rs11161693	0.91[CHB][hapmap]
rs11161695	0.91[CHB][hapmap]
rs11161696	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs11161697	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12029238	0.95[CHB][hapmap]
rs1564516	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17411495	0.95[CHB][hapmap]
rs1904947	0.95[CHB][hapmap]
rs193398	0.83[CEU][hapmap]
rs2892901	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs313698	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs313700	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs313701	0.91[CHB][hapmap]
rs313702	0.91[CHB][hapmap]
rs313703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs313704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs313705	0.91[CHB][hapmap]
rs313706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs313707	0.91[CHB][hapmap]
rs313708	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs313709	0.91[CHB][hapmap]
rs313733	0.83[CEU][hapmap]
rs313735	0.83[CEU][hapmap]
rs313738	0.91[CHB][hapmap]
rs313740	0.87[CHB][hapmap]
rs313741	0.86[CHB][hapmap]
rs313742	0.87[CHB][hapmap]
rs313746	0.86[CHB][hapmap]
rs313747	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313748	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313756	0.87[CHB][hapmap]
rs313757	0.91[CHB][hapmap]
rs313758	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313763	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs313769	0.95[CHB][hapmap]
rs313770	0.95[CHB][hapmap]
rs313771	0.95[CHB][hapmap]
rs313773	0.87[ASN][1000 genomes]
rs313775	0.95[CHB][hapmap]
rs412328	0.83[CEU][hapmap]
rs428475	0.95[CHB][hapmap]
rs432168	0.83[CEU][hapmap]
rs435007	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs437257	0.95[CHB][hapmap]
rs482789	0.86[CHB][hapmap]
rs537408	0.86[CHB][hapmap]
rs573444	0.81[CHB][hapmap]
rs593146	0.80[CHB][hapmap]
rs629140	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6576793	1.00[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs673506	0.83[CEU][hapmap]
rs7524286	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7536101	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs186376	LRP10	trans	parietal	SCAN
rs186376	ANKS6	trans	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86280000-86296600	Weak transcription	GM12878-XiMat	blood
2	chr1:86283600-86296400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86284000-86296400	Weak transcription	Fetal Lung	lung
4	chr1:86284200-86296400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:86284200-86296400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:86284600-86288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86284800-86286600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:86285800-86287200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:86286000-86286600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:86286000-86286600	Enhancers	Adipose Nuclei	Adipose
11	chr1:86286200-86286600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:86286400-86287000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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