Variant report

Variant	rs11601553
Chromosome Location	chr11:86498414-86498415
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86496364..86499303-chr11:86500997..86503466,3	K562	blood:
2	chr11:45825293..45827248-chr11:86498185..86501073,2	MCF-7	breast:
3	chr11:86452587..86455678-chr11:86498398..86501247,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181830	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1075702	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11234795	0.81[ASN][1000 genomes]
rs11234809	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11602695	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12361769	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12366016	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12420039	0.86[CHB][hapmap]
rs12421517	0.85[ASN][1000 genomes]
rs12421942	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12797648	0.95[ASN][1000 genomes]
rs12802848	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12809023	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17211926	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17819068	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17819134	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17819181	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs17819187	0.86[CHB][hapmap]
rs1807014	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1939110	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs1939111	0.86[CHB][hapmap]
rs1939112	0.91[CHB][hapmap]
rs1939113	0.85[CHB][hapmap]
rs1939114	0.86[CHB][hapmap]
rs1939115	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1939116	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1939117	0.98[ASN][1000 genomes]
rs1954769	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2155081	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs2433433	0.86[JPT][hapmap]
rs2433434	0.86[JPT][hapmap]
rs2433435	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2433436	0.86[JPT][hapmap]
rs2433438	0.86[JPT][hapmap]
rs2433439	0.86[JPT][hapmap]
rs2513018	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs3096715	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3096716	0.86[JPT][hapmap]
rs34833002	0.86[ASN][1000 genomes]
rs35902217	0.98[ASN][1000 genomes]
rs36061072	0.98[ASN][1000 genomes]
rs3809048	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4128368	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4245427	0.87[ASN][1000 genomes]
rs4269941	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4304806	0.86[CHB][hapmap]
rs4307743	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4423210	0.86[CHB][hapmap]
rs4450192	0.84[ASN][1000 genomes]
rs4485132	0.91[CHB][hapmap]
rs4495915	0.94[ASN][1000 genomes]
rs4570601	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943958	0.88[ASN][1000 genomes]
rs4943959	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4943960	0.85[ASN][1000 genomes]
rs4944630	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4944631	0.88[ASN][1000 genomes]
rs4944632	0.88[ASN][1000 genomes]
rs4944633	0.86[ASN][1000 genomes]
rs4944634	0.85[ASN][1000 genomes]
rs55646317	0.97[ASN][1000 genomes]
rs58976693	0.97[ASN][1000 genomes]
rs59850783	0.85[ASN][1000 genomes]
rs60023003	0.86[ASN][1000 genomes]
rs61690902	0.81[ASN][1000 genomes]
rs61707378	0.96[ASN][1000 genomes]
rs6592315	0.93[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105467	0.93[ASN][1000 genomes]
rs7120185	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120320	0.89[ASN][1000 genomes]
rs7123349	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7126492	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7131625	0.86[CHB][hapmap]
rs744292	0.97[ASN][1000 genomes]
rs7926235	0.88[ASN][1000 genomes]
rs7926713	0.82[ASN][1000 genomes]
rs7926946	0.81[ASN][1000 genomes]
rs7927257	0.81[ASN][1000 genomes]
rs7927479	0.82[ASN][1000 genomes]
rs7940201	0.95[ASN][1000 genomes]
rs7942344	0.88[ASN][1000 genomes]
rs7948063	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs7950776	0.84[ASN][1000 genomes]
rs7951582	0.86[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]

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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11601553	CCDC89	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86487400-86501400	Weak transcription	Ovary	ovary
2	chr11:86493000-86502200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:86495400-86510400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:86495600-86501000	Weak transcription	A549	lung
5	chr11:86495800-86501000	Weak transcription	Fetal Kidney	kidney
6	chr11:86496200-86499400	Enhancers	Fetal Intestine Large	intestine
7	chr11:86496200-86499400	Enhancers	Fetal Intestine Small	intestine
8	chr11:86496600-86501400	Weak transcription	Fetal Lung	lung
9	chr11:86496600-86502000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:86497000-86500000	Weak transcription	Hela-S3	cervix
11	chr11:86497000-86510000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:86497200-86498800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:86497200-86501600	Weak transcription	HSMMtube	muscle
14	chr11:86497800-86498600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr11:86497800-86499000	Enhancers	Duodenum Mucosa	Duodenum

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