Variant report

Variant	rs12370130
Chromosome Location	chr12:119784124-119784125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:119764864..119767176-chr12:119782140..119784942,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10774492	0.93[ASN][1000 genomes]
rs10774496	0.80[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs10849647	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849651	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs10849652	0.80[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849653	0.82[ASN][1000 genomes]
rs10849656	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10849657	0.85[JPT][hapmap]
rs10849659	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs11064751	0.82[AMR][1000 genomes]
rs11064757	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11064761	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11064763	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11064764	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12367398	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4300442	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs4465416	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4991185	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs56686166	0.81[ASN][1000 genomes]
rs7301599	0.90[CHD][hapmap]
rs7313792	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs73404383	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv1047036	chr12:119477583-119992640	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv832528	chr12:119638211-119793401	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899552	chr12:119733874-119814623	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12370130	PXN	cis	cerebellum	SCAN
rs12370130	HSPB8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:119781000-119784200	Weak transcription	Fetal Brain Female	brain

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