Variant report

Variant	rs199124
Chromosome Location	chr6:23562269-23562270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1000105	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014989	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12193599	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12200767	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12201667	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12213279	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12215692	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17499234	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17499906	0.87[ASN][1000 genomes]
rs17499955	0.83[ASN][1000 genomes]
rs1923197	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923198	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs197966	0.80[ASN][1000 genomes]
rs197968	0.80[ASN][1000 genomes]
rs199079	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs199081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57279011	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58834120	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59488676	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456557	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917610	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7746629	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7746858	0.83[EUR][1000 genomes]
rs7754459	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7766899	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs877615	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9466849	0.83[EUR][1000 genomes]
rs9466850	0.84[EUR][1000 genomes]
rs9466852	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422291	chr6:23466080-23600459	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv830608	chr6:23558655-23644405	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs199124	HIST1H2AA	cis	parietal	SCAN
rs199124	HIST1H2BB	cis	cerebellum	SCAN
rs199124	ACOT13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:23561200-23562400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:23561800-23562400	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr6:23561800-23562600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:23561800-23562800	ZNF genes & repeats	Liver	Liver
5	chr6:23562000-23562400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links