Variant report

Variant	rs313708
Chromosome Location	chr1:86318888-86318889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1072508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1072509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873730	1.00[CHB][hapmap]
rs10873731	0.91[CHB][hapmap]
rs11161693	0.95[CHB][hapmap]
rs11161695	0.95[CHB][hapmap]
rs11161696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161697	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029238	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12124109	0.84[ASN][1000 genomes]
rs12127479	0.82[ASN][1000 genomes]
rs12144570	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1564516	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17411495	1.00[CHB][hapmap];0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs186376	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]
rs1904947	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2256515	0.82[ASN][1000 genomes]
rs2795038	0.82[ASN][1000 genomes]
rs2892901	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313698	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs313700	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313701	0.95[CHB][hapmap]
rs313702	0.95[CHB][hapmap]
rs313703	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313704	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313705	0.95[CHB][hapmap]
rs313706	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs313707	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs313709	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs313738	0.95[CHB][hapmap]
rs313740	0.91[CHB][hapmap]
rs313741	0.91[CHB][hapmap]
rs313742	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs313746	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs313747	0.86[ASN][1000 genomes]
rs313748	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs313756	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs313757	0.95[CHB][hapmap]
rs313758	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs313759	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs313763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313764	0.82[ASN][1000 genomes]
rs313766	0.82[ASN][1000 genomes]
rs313768	0.82[ASN][1000 genomes]
rs313769	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs313770	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs313771	1.00[CHB][hapmap]
rs313773	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313774	0.82[ASN][1000 genomes]
rs313775	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs383588	0.81[ASN][1000 genomes]
rs428475	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs435007	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437257	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs445782	0.84[ASN][1000 genomes]
rs482789	0.91[CHB][hapmap]
rs537408	0.91[CHB][hapmap]
rs556247	0.82[ASN][1000 genomes]
rs573444	0.86[CHB][hapmap]
rs593146	0.85[CHB][hapmap]
rs629140	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576793	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524286	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7536101	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs7544141	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv871189	chr1:86315724-86402244	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs313708	SAMD13	cis	cerebellum	SCAN
rs313708	LRP10	trans	parietal	SCAN
rs313708	HS2ST1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86305000-86332600	Weak transcription	Fetal Lung	lung
2	chr1:86305200-86326600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:86316600-86322200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86316600-86326400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:86316600-86327400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links