Variant report

Variant	rs12145163
Chromosome Location	chr1:210688784-210688785
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10489385	1.00[ASW][hapmap]
rs10779529	0.83[AFR][1000 genomes]
rs11119487	0.83[AFR][1000 genomes]
rs12028017	0.83[AFR][1000 genomes]
rs12035213	0.83[AFR][1000 genomes]
rs12117750	0.92[CEU][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12119268	0.83[AFR][1000 genomes]
rs12124208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12142231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12143482	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12143703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17260431	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17260438	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17260466	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765848	0.83[AFR][1000 genomes]
rs3765853	0.83[AFR][1000 genomes]
rs3819985	1.00[ASW][hapmap];0.83[AFR][1000 genomes]
rs4253918	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4620549	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55726579	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55780618	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6540599	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873147	chr1:210665583-210696806	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12145163	INTS7	cis	cerebellum	SCAN
rs12145163	CNTN2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210674400-210719600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210679800-210689400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:210680600-210731000	Weak transcription	HSMM	muscle
4	chr1:210685600-210689400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:210685800-210689800	Weak transcription	Pancreas	Pancrea
6	chr1:210687200-210689600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:210688400-210699600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links