Variant report

Variant	rs5896
Chromosome Location	chr11:46745003-46745004
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	chr11:46738555..46741511-chr11:46744742..46747329,2	K562	blood:
2	chr11:46722213..46727380-chr11:46743173..46747634,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175213	Chromatin interaction
ENSG00000180210	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1007738	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10734548	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10769211	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10838612	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11038977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039002	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11039014	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11602036	0.84[AMR][1000 genomes]
rs11602537	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604876	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574512	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12575609	0.81[AMR][1000 genomes]
rs1551744	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs1799867	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2070851	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2306028	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2306033	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2306036	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2306037	1.00[JPT][hapmap]
rs3136441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3136449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136457	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136458	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3136460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136499	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4294527	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4453193	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs4453194	0.85[AMR][1000 genomes]
rs4491174	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4534535	0.87[AMR][1000 genomes]
rs4603265	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4752927	0.82[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap]
rs4752931	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752933	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs4752946	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4752947	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs57704144	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58561056	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58922799	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61337452	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7101374	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7107778	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7929294	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs7940441	0.82[JPT][hapmap]
rs964551	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv897322	chr11:46739748-46748916	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv3474063	chr11:46740876-46745174	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3474074	chr11:46740876-46745174	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5896	ACP2	cis	lymphoblastoid	seeQTL
rs5896	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs5896	PTPMT1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46728800-46745600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:46728800-46745600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:46739800-46745600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:46740200-46745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:46740200-46745600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:46740400-46745600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:46741800-46746800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:46742000-46745600	Weak transcription	A549	lung
9	chr11:46744000-46745400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:46744400-46752000	Genic enhancers	Liver	Liver
11	chr11:46744800-46745400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:46745000-46745400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:46745000-46751200	Genic enhancers	HepG2	liver

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