Variant report

Variant	rs2788282
Chromosome Location	chr6:101920506-101920507
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1832415	1.00[YRI][hapmap]
rs2248237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248950	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs2249263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2252682	0.81[CHB][hapmap]
rs2255496	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2518155	1.00[YRI][hapmap]
rs2518160	1.00[YRI][hapmap]
rs2518166	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2518167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2518168	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2518169	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2518170	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2518171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap]
rs2518185	1.00[YRI][hapmap]
rs2518229	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2518232	0.83[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2518233	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2579935	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2579939	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2788279	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2788280	0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2852533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv886459	chr6:101880376-101951502	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886460	chr6:101890395-101951502	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv886461	chr6:101916765-101948788	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv886462	chr6:101916765-101951502	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2788282	SIM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101903400-101921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links