Variant report

Variant	rs12577739
Chromosome Location	chr11:85941394-85941395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85935426..85937686-chr11:85939503..85941915,2	MCF-7	breast:
2	chr11:85939907..85943169-chr11:85949863..85954103,4	K562	blood:
3	chr11:85445751..85448371-chr11:85941133..85943891,2	MCF-7	breast:
4	chr11:85941376..85943458-chr11:85954441..85957343,3	MCF-7	breast:
5	chr11:85940546..85944028-chr11:85951263..85955917,6	K562	blood:
6	chr11:85940346..85942703-chr11:85944829..85946425,2	K562	blood:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10792840	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898445	0.81[CEU][hapmap]
rs10898450	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898454	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898455	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898456	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11234582	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11234585	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11234586	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11234587	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11234591	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11234592	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11234595	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1215001	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12225782	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12226796	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12282663	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12574118	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12800606	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1376947	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1391221	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs19039	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2847470	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs291215	0.90[CHB][hapmap]
rs291216	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs291220	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs291221	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs291225	0.80[EUR][1000 genomes]
rs291227	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs291228	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs291230	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs291231	0.81[EUR][1000 genomes]
rs291232	0.81[EUR][1000 genomes]
rs291233	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs291234	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs291235	0.82[EUR][1000 genomes]
rs291237	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs291238	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs291242	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs291251	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34095340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34972740	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3923738	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4547120	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4944562	0.93[EUR][1000 genomes]
rs57902302	0.84[ASN][1000 genomes]
rs61178383	0.81[ASN][1000 genomes]
rs7106569	0.91[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12577739	EED	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85938400-85941400	Weak transcription	Placenta	Placenta
2	chr11:85939400-85942400	Enhancers	Hela-S3	cervix
3	chr11:85939600-85942600	Enhancers	HMEC	breast
4	chr11:85939600-85942800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:85939800-85942000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:85939800-85942400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:85939800-85942600	Enhancers	NHEK	skin
8	chr11:85940000-85942600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:85941000-85941400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:85941000-85941600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr11:85941000-85943600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:85941200-85941600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr11:85941200-85941600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:85941200-85941600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr11:85941200-85941600	Enhancers	Brain Anterior Caudate	brain
16	chr11:85941200-85941600	Enhancers	Colonic Mucosa	Colon
17	chr11:85941200-85941600	Enhancers	Stomach Smooth Muscle	stomach
18	chr11:85941200-85941800	Enhancers	K562	blood
19	chr11:85941200-85942400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:85941200-85942400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:85941200-85942600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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