Variant report

Variant	rs12988978
Chromosome Location	chr2:116055374-116055375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12616456	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617588	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12617785	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12619497	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12619606	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12991665	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12993170	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12998960	0.81[ASN][1000 genomes]
rs13005522	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13009552	0.83[ASN][1000 genomes]
rs13011541	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13018318	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13018346	0.80[EUR][1000 genomes]
rs13027054	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13027383	0.80[EUR][1000 genomes]
rs13031722	0.82[ASN][1000 genomes]
rs13032365	1.00[JPT][hapmap]
rs17044243	0.80[EUR][1000 genomes]
rs34168937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34195762	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34423273	0.80[EUR][1000 genomes]
rs34553628	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34777388	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34787934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34911120	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34938977	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35363264	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35672000	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4399739	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71418540	0.83[ASN][1000 genomes]
rs71418546	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71418547	0.83[EUR][1000 genomes]
rs71418548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71418549	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs71418550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71418551	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs71418552	0.80[EUR][1000 genomes]
rs71418553	0.80[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	nsv1001542	chr2:115920847-116082585	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv834339	chr2:115953298-116132979	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:116050800-116068000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:116052800-116056000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:116053400-116056400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:116053800-116056200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:116054000-116057000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:116055200-116055400	Enhancers	HUES48 Cell Line	embryonic stem cell

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