Variant report

Variant	rs560474
Chromosome Location	chr11:86949985-86949986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10501633	0.86[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs11494237	0.86[CEU][hapmap]
rs1686166	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs1785603	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs1791446	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs2509560	0.86[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs470149	0.83[EUR][1000 genomes]
rs470527	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs470706	0.86[CEU][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs470810	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs470820	0.82[EUR][1000 genomes]
rs470828	0.86[CEU][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs492373	0.83[EUR][1000 genomes]
rs511056	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs518557	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518921	0.83[EUR][1000 genomes]
rs519308	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs526023	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs529720	0.83[EUR][1000 genomes]
rs529831	0.86[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs550503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553446	0.86[CEU][hapmap];0.95[YRI][hapmap]
rs554554	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs569494	0.82[EUR][1000 genomes]
rs571350	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs575166	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs614269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629078	0.83[EUR][1000 genomes]
rs643937	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs645709	0.83[EUR][1000 genomes]
rs645710	0.83[EUR][1000 genomes]
rs657917	0.86[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs658369	0.86[CEU][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs663362	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv468777	chr11:86794856-86985581	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv555707	chr11:86794856-86985581	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv468778	chr11:86850483-86974576	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv555708	chr11:86850483-86974576	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv898065	chr11:86891077-86984439	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv898066	chr11:86891077-86989134	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv468779	chr11:86928253-87001892	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv555709	chr11:86928253-87001892	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv898068	chr11:86930270-87005969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	nsv898069	chr11:86932603-86984439	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
20	nsv898070	chr11:86932603-86989134	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
21	nsv555710	chr11:86947024-87001892	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs560474	CCDC89	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86943800-86950600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:86945000-86952400	Weak transcription	HepG2	liver
3	chr11:86947400-86952000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:86948000-86951000	Weak transcription	Aorta	Aorta
5	chr11:86948200-86950000	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:86949400-86950400	Enhancers	Osteobl	bone
7	chr11:86949600-86950000	Enhancers	Rectal Smooth Muscle	rectum
8	chr11:86949600-86950200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:86949800-86950200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:86949800-86950200	Flanking Active TSS	HUVEC	blood vessel
11	chr11:86949800-86950400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr11:86949800-86950400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:86949800-86951200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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