Variant report

Variant	rs2568029
Chromosome Location	chr11:8927518-8927519
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	chr11:8925893..8928872-chr11:8930220..8933061,3	MCF-7	breast:
2	chr11:8903715..8906519-chr11:8925903..8928507,2	K562	blood:

Variant related genes	Relation type
ENSG00000166452	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10734638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840127	0.94[CEU][hapmap]
rs10840129	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs11042099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1133833	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs1136966	0.90[MEX][hapmap]
rs12794962	0.86[MEX][hapmap]
rs16906056	0.88[CEU][hapmap]
rs16906614	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17337866	0.94[CEU][hapmap]
rs1811367	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2016844	0.81[MEX][hapmap]
rs2056903	0.81[MEX][hapmap]
rs2060157	0.89[EUR][1000 genomes]
rs2116510	0.86[MEX][hapmap]
rs2163625	0.86[MEX][hapmap]
rs2568035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568042	0.87[YRI][hapmap]
rs2568047	0.86[MEX][hapmap]
rs2568056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568078	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2653556	0.82[MEX][hapmap]
rs2653558	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653565	0.90[MEX][hapmap]
rs2653566	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653601	0.81[MEX][hapmap]
rs2653604	0.81[MEX][hapmap]
rs2653609	0.84[EUR][1000 genomes]
rs2653618	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742483	0.87[EUR][1000 genomes]
rs2742493	0.81[MEX][hapmap]
rs2742496	0.80[MEX][hapmap]
rs2742497	0.81[MEX][hapmap]
rs2742502	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs2742521	0.85[YRI][hapmap]
rs2742549	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742553	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34152382	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34275210	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34371023	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34418236	0.82[EUR][1000 genomes]
rs34581555	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34769330	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35503692	0.81[EUR][1000 genomes]
rs35563381	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35580466	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35909878	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36094920	0.80[EUR][1000 genomes]
rs36100955	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36180552	0.82[EUR][1000 genomes]
rs3751068	0.81[MEX][hapmap]
rs3850934	0.92[CEU][hapmap]
rs3915868	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs4370967	0.82[MEX][hapmap]
rs4910068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7110170	0.81[EUR][1000 genomes]
rs7117900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7125458	0.86[MEX][hapmap]
rs7127197	0.80[EUR][1000 genomes]
rs7936201	0.95[MEX][hapmap]
rs7950491	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2568029	PRKCDBP	cis	parietal	SCAN
rs2568029	RPL27A	cis	cerebellum	SCAN
rs2568029	RPL27A	cis	parietal	SCAN
rs2568029	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs2568029	TMEM9B	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8926000-8929400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:8926600-8928400	Enhancers	A549	lung
3	chr11:8926600-8929000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:8926600-8929000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr11:8926600-8929000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:8926600-8929000	Enhancers	HMEC	breast
7	chr11:8926600-8930000	Enhancers	NHEK	skin
8	chr11:8926800-8928400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:8926800-8929400	Enhancers	NHLF	lung
10	chr11:8927000-8928200	Enhancers	Placenta	Placenta
11	chr11:8927000-8928800	Enhancers	HSMMtube	muscle
12	chr11:8927000-8929000	Enhancers	Osteobl	bone
13	chr11:8927200-8928800	Enhancers	HSMM	muscle
14	chr11:8927200-8929000	Enhancers	NHDF-Ad	bronchial
15	chr11:8927200-8931000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:8927400-8927600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:8927400-8927600	Enhancers	Hela-S3	cervix
18	chr11:8927400-8927600	Flanking Active TSS	NH-A	brain
19	chr11:8927400-8927800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:8927400-8928200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:8927400-8929000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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