Variant report

Variant	rs650826
Chromosome Location	chr11:49250912-49250913
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:49250422..49251012-chr11:49547571..49548253,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10734597	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10742937	0.84[ASN][1000 genomes]
rs10769571	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769573	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10839217	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs10839248	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10839251	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10839253	0.91[ASN][1000 genomes]
rs10839254	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10839255	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10839257	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10839259	0.81[ASN][1000 genomes]
rs10839270	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs11040241	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs11040255	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap]
rs11040261	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs11040289	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11040311	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11040322	0.92[ASN][1000 genomes]
rs11040359	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs11822117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11823826	0.91[ASN][1000 genomes]
rs11827867	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12221758	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1819409	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap]
rs1851981	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872610	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs191862	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2005014	0.91[ASN][1000 genomes]
rs202672	0.81[ASN][1000 genomes]
rs202673	0.81[ASN][1000 genomes]
rs202681	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs202687	0.81[ASN][1000 genomes]
rs202689	0.84[ASN][1000 genomes]
rs202695	0.85[ASN][1000 genomes]
rs202696	0.85[ASN][1000 genomes]
rs202698	0.86[ASN][1000 genomes]
rs202701	0.85[ASN][1000 genomes]
rs202705	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs202713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs202719	0.82[ASN][1000 genomes]
rs202724	0.81[ASN][1000 genomes]
rs2200497	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2866347	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2903253	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2931177	0.91[ASN][1000 genomes]
rs369803	0.82[ASN][1000 genomes]
rs3881244	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3881245	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4088771	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4303234	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4373925	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595139	0.82[ASN][1000 genomes]
rs596754	1.00[ASN][1000 genomes]
rs597683	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600974	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs611931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613429	0.94[ASN][1000 genomes]
rs613450	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636059	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6485971	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs648728	0.84[ASN][1000 genomes]
rs651278	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs677785	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs689329	0.84[ASN][1000 genomes]
rs7103267	0.92[ASN][1000 genomes]
rs7103270	0.92[ASN][1000 genomes]
rs7106905	0.92[ASN][1000 genomes]
rs7111262	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114817	0.91[ASN][1000 genomes]
rs7115507	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117025	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7118094	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7118378	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7118379	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7121968	0.91[ASN][1000 genomes]
rs7122073	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7125691	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131181	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131190	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7481212	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7925859	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7932738	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs7935256	0.81[EUR][1000 genomes];0.88[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	nsv469956	chr11:48922645-49862647	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv554347	chr11:49111467-49862647	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1044070	chr11:49147743-49448774	Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv525454	chr11:49156039-49570587	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv518571	chr11:49162948-49627833	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758269	chr11:49212237-49468966	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2759825	chr11:49212237-49468966	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv972016	chr11:49246163-49330536	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs650826	SLC35C1	cis	cerebellum	SCAN
rs650826	OR4C3	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:49245200-49254600	Weak transcription	Fetal Intestine Small	intestine
2	chr11:49245400-49251000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:49247200-49251000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links