Variant report

Variant	rs12420039
Chromosome Location	chr11:86528437-86528438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45823561..45828126-chr11:86528256..86531993,4	MCF-7	breast:
2	chr11:86510061..86515412-chr11:86524967..86529841,8	MCF-7	breast:
3	chr11:86487507..86489179-chr11:86528205..86530836,2	MCF-7	breast:
4	chr11:86527774..86530543-chr11:86627685..86629323,2	MCF-7	breast:
5	chr11:86525218..86527255-chr11:86527296..86529166,3	MCF-7	breast:
6	chr11:86456277..86457862-chr11:86528085..86530264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181830	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11601553	0.86[CHB][hapmap]
rs11602695	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12421517	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12421942	0.81[ASN][1000 genomes]
rs12574979	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12802848	0.82[CHB][hapmap]
rs17211787	0.93[MEX][hapmap]
rs17211926	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs17212012	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17819068	0.87[CEU][hapmap];0.87[CHB][hapmap]
rs17819134	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs17819181	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17819187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939110	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1939111	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939112	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1939113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939116	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1954769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005192	0.82[CHB][hapmap]
rs2155080	0.94[ASN][1000 genomes]
rs2155081	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2433431	0.80[MEX][hapmap]
rs2433432	0.80[MEX][hapmap]
rs2433433	0.80[MEX][hapmap]
rs2433434	0.80[MEX][hapmap]
rs2433439	0.86[MEX][hapmap]
rs2513003	0.80[MEX][hapmap]
rs28517777	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4128368	0.91[CHB][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs4269941	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs4291699	0.93[ASN][1000 genomes]
rs4304806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4307743	0.82[CHB][hapmap]
rs4307748	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4423210	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4485132	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4495915	1.00[CEU][hapmap]
rs4570601	0.82[CHB][hapmap]
rs4944630	0.82[CHB][hapmap]
rs55646317	0.85[AMR][1000 genomes]
rs58512185	0.88[AMR][1000 genomes]
rs58976693	0.85[AMR][1000 genomes]
rs61707378	0.86[AMR][1000 genomes]
rs6592315	0.82[CHB][hapmap]
rs7108490	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118751	0.99[ASN][1000 genomes]
rs7126492	0.86[CHB][hapmap]
rs7131625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs744292	0.85[AMR][1000 genomes]
rs7931274	0.97[ASN][1000 genomes]
rs7948063	0.82[CHB][hapmap]
rs7951582	0.82[CHB][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	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	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
4	nsv523704	chr11:86508928-86528437	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2760199	chr11:86512312-86531118	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86514000-86530000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:86517200-86529800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:86520000-86549200	Weak transcription	Ovary	ovary
4	chr11:86521000-86551400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:86522800-86544400	Weak transcription	Fetal Kidney	kidney
6	chr11:86525200-86528800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr11:86525200-86529200	Enhancers	HSMM	muscle
8	chr11:86525200-86530400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr11:86525200-86531000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:86525600-86529400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:86525800-86530200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:86525800-86530400	Enhancers	Hela-S3	cervix
13	chr11:86525800-86530800	Enhancers	Rectal Smooth Muscle	rectum
14	chr11:86526000-86529400	Weak transcription	Fetal Heart	heart
15	chr11:86526000-86529400	Weak transcription	Fetal Lung	lung
16	chr11:86526400-86529000	Weak transcription	Fetal Muscle Leg	muscle
17	chr11:86526800-86530200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:86526800-86531000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:86527200-86528800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:86527400-86529800	Weak transcription	Aorta	Aorta
21	chr11:86527400-86530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:86527400-86530000	Weak transcription	Right Atrium	heart
23	chr11:86527400-86530200	Enhancers	HSMMtube	muscle
24	chr11:86527400-86530400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:86527400-86531000	Enhancers	Colon Smooth Muscle	Colon
26	chr11:86527600-86528600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:86527600-86528800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:86527600-86528800	Weak transcription	NHLF	lung
29	chr11:86527600-86529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:86527600-86529000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:86527600-86529800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:86527800-86528800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:86527800-86528800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:86527800-86528800	Weak transcription	NHDF-Ad	bronchial
35	chr11:86527800-86529000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:86527800-86529000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:86527800-86529000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:86527800-86529000	Weak transcription	NHEK	skin
39	chr11:86527800-86529400	Weak transcription	Fetal Stomach	stomach
40	chr11:86527800-86529800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:86527800-86530400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:86527800-86534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:86528000-86528600	Weak transcription	Osteobl	bone
44	chr11:86528000-86529000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:86528000-86529000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:86528000-86529000	Enhancers	A549	lung
47	chr11:86528000-86529800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:86528000-86530200	Enhancers	HUVEC	blood vessel
49	chr11:86528000-86530400	Enhancers	NH-A	brain
50	chr11:86528000-86542600	Weak transcription	Adipose Nuclei	Adipose

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