Variant report

Variant	rs12284270
Chromosome Location	chr11:57580266-57580267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57508369..57511140-chr11:57577565..57580322,2	MCF-7	breast:
2	chr11:57570082..57573080-chr11:57578840..57580964,2	MCF-7	breast:
3	chr11:57568699..57575383-chr11:57575572..57580605,8	K562	blood:

Variant related genes	Relation type
ENSG00000254732	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000211450	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10896641	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11570214	0.98[AFR][1000 genomes]
rs11570222	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11827268	1.00[ASN][1000 genomes]
rs1704778	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2911726	1.00[YRI][hapmap]
rs2926651	0.82[AFR][1000 genomes]
rs2926652	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2926657	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956979	0.82[AFR][1000 genomes]
rs2969934	1.00[YRI][hapmap]
rs2969940	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2969946	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs593915	1.00[ASN][1000 genomes]
rs613152	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs620450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs637770	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs686459	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12284270	CTNND1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57556400-57587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57568200-57585800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:57568200-57586000	Strong transcription	Fetal Muscle Leg	muscle
4	chr11:57568200-57588200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:57568400-57586600	Strong transcription	Placenta	Placenta
6	chr11:57568600-57581000	Strong transcription	K562	blood
7	chr11:57568600-57585800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:57568600-57586000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:57568600-57586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:57568600-57586400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:57568600-57586600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:57568600-57587000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:57568600-57587200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:57568600-57589000	Strong transcription	NHLF	lung
15	chr11:57568800-57585200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr11:57568800-57585600	Strong transcription	Fetal Intestine Large	intestine
17	chr11:57568800-57589000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:57568800-57589000	Strong transcription	NH-A	brain
19	chr11:57569000-57580600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr11:57569000-57583800	Strong transcription	NHDF-Ad	bronchial
21	chr11:57569000-57584800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:57569000-57584800	Strong transcription	HMEC	breast
23	chr11:57569000-57585000	Strong transcription	HepG2	liver
24	chr11:57569000-57585800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr11:57569000-57586000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:57569000-57586400	Strong transcription	Brain Germinal Matrix	brain
27	chr11:57569000-57587000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:57569000-57587000	Strong transcription	NHEK	skin
29	chr11:57569000-57587200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr11:57569000-57587400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:57569000-57587800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:57569000-57588800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:57569000-57589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:57569200-57580400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:57569200-57580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:57569200-57581200	Strong transcription	Hela-S3	cervix
37	chr11:57569200-57583200	Strong transcription	Fetal Brain Male	brain
38	chr11:57569200-57584800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:57569200-57584800	Strong transcription	A549	lung
40	chr11:57569200-57585000	Strong transcription	Ovary	ovary
41	chr11:57569200-57585200	Strong transcription	Fetal Intestine Small	intestine
42	chr11:57569200-57585400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:57569200-57585400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr11:57569200-57585800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:57569200-57585800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:57569200-57585800	Strong transcription	Fetal Stomach	stomach
47	chr11:57569200-57585800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:57569200-57586000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:57569200-57586200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:57569200-57586200	Strong transcription	Primary monocytes fromperipheralblood	blood

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