Variant report

Variant	rs1351952
Chromosome Location	chr8:120117168-120117169
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	chr8:120116952..120120158-chr8:120220292..120221972,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147676	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1158945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11994775	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13259300	0.84[ASN][1000 genomes]
rs1385493	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1485290	0.81[CEU][hapmap]
rs1485291	0.81[CEU][hapmap]
rs1485293	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1485294	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1905775	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2242313	0.82[JPT][hapmap]
rs2450060	0.85[GIH][hapmap]
rs2450063	0.89[GIH][hapmap]
rs2450064	0.83[CEU][hapmap];0.90[ASN][1000 genomes]
rs2450065	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2450067	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2450068	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2450069	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2450072	0.82[JPT][hapmap]
rs2450076	0.82[JPT][hapmap]
rs2450079	0.89[GIH][hapmap]
rs2450080	0.82[JPT][hapmap]
rs2465385	0.81[JPT][hapmap]
rs2465390	0.86[JPT][hapmap]
rs2465392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465403	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2465404	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2468171	0.86[CEU][hapmap]
rs7386676	0.81[CEU][hapmap]
rs7813952	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv612057	chr8:120109439-120118617	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1351952	TNFRSF11B	cis	lymphoblastoid	seeQTL
rs1351952	MAL2	cis	cerebellum	SCAN
rs1351952	NOV	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120103800-120117400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:120112000-120119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:120115000-120118000	Weak transcription	Lung	lung
4	chr8:120115200-120121000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:120116600-120119400	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links