Variant report

Variant	rs4978511
Chromosome Location	chr9:115654246-115654247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115653409..115654935-chr9:115663870..115665546,2	MCF-7	breast:
2	chr9:115653737..115657233-chr9:115662868..115665778,3	K562	blood:
3	chr9:115647367..115649652-chr9:115652587..115654849,2	MCF-7	breast:
4	chr9:115653499..115655772-chr9:115659487..115662405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271631	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10115576	0.82[CEU][hapmap]
rs10115711	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10124939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124979	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10481638	0.81[GIH][hapmap]
rs10732374	0.81[GIH][hapmap]
rs10733595	0.81[GIH][hapmap]
rs10733596	0.81[GIH][hapmap]
rs10733598	0.82[CEU][hapmap]
rs10733599	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10739371	0.81[GIH][hapmap]
rs10739373	0.88[GIH][hapmap]
rs10739376	0.82[CEU][hapmap]
rs10739378	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10739379	0.89[ASN][1000 genomes]
rs10739380	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759590	0.82[CEU][hapmap]
rs10759596	0.81[GIH][hapmap]
rs10759598	0.81[GIH][hapmap]
rs10759603	0.82[CEU][hapmap]
rs10817398	0.81[GIH][hapmap]
rs1158331	0.98[EUR][1000 genomes]
rs1324931	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs1475293	0.82[CEU][hapmap]
rs1539342	0.81[GIH][hapmap]
rs1570754	0.96[EUR][1000 genomes]
rs2025544	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2147646	0.98[EUR][1000 genomes]
rs2182048	0.96[EUR][1000 genomes]
rs4304397	0.88[GIH][hapmap]
rs4360356	0.98[EUR][1000 genomes]
rs4978510	0.83[EUR][1000 genomes]
rs4979163	0.81[GIH][hapmap]
rs4979170	0.82[CEU][hapmap]
rs4979176	0.89[ASN][1000 genomes]
rs4979183	0.96[EUR][1000 genomes]
rs4979184	0.96[EUR][1000 genomes]
rs4979186	0.96[EUR][1000 genomes]
rs61742087	0.89[ASN][1000 genomes]
rs7026450	0.96[EUR][1000 genomes]
rs7040954	0.96[EUR][1000 genomes]
rs7856199	0.81[GIH][hapmap]
rs7869100	0.83[EUR][1000 genomes]
rs787299	0.88[GIH][hapmap]
rs7873289	0.82[CEU][hapmap]
rs912662	0.98[EUR][1000 genomes]
rs980345	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
6	esv2757352	chr9:115648457-115664299	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv529036	chr9:115652836-115655849	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4978511	TSCOT	cis	multi-tissue	Pritchard
rs4978511	PTPRG	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115653200-115654400	Weak transcription	Gastric	stomach
2	chr9:115653200-115659000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr9:115653400-115656000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:115653600-115654800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:115653600-115655600	Weak transcription	Osteobl	bone
6	chr9:115654000-115656600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links