Variant report

Variant	rs55642252
Chromosome Location	chr11:86346223-86346224
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86336049..86341479-chr11:86341893..86346875,7	MCF-7	breast:
2	chr11:86345451..86347957-chr11:86512981..86515684,2	MCF-7	breast:
3	chr11:86343672..86346376-chr11:86522786..86524329,2	MCF-7	breast:
4	chr11:86342318..86349364-chr11:86509780..86514935,13	MCF-7	breast:
5	chr11:86341794..86343569-chr11:86345090..86348008,2	MCF-7	breast:
6	chr11:86345410..86347094-chr11:86347295..86350272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10501624	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10501625	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12099044	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12292032	1.00[ASN][1000 genomes]
rs17149180	1.00[ASN][1000 genomes]
rs17149223	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149226	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149234	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149238	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149242	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149245	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149305	0.87[AMR][1000 genomes]
rs17149308	0.87[AMR][1000 genomes]
rs17149311	0.87[AMR][1000 genomes]
rs17149326	0.81[AMR][1000 genomes]
rs1945141	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156532	1.00[ASN][1000 genomes]
rs34662182	1.00[ASN][1000 genomes]
rs4614483	1.00[ASN][1000 genomes]
rs55763915	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55894714	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048600	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56056120	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56272084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56304616	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58173252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58968600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59227416	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59339534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59415795	1.00[ASN][1000 genomes]
rs61182121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61230561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61248687	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61372386	1.00[ASN][1000 genomes]
rs7103556	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103642	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72961775	1.00[ASN][1000 genomes]
rs73514376	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73526075	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73526086	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73528019	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940187	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940523	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7941124	1.00[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	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv520466	chr11:86344677-86346940	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86333200-86349800	Weak transcription	Esophagus	oesophagus
2	chr11:86336000-86348000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:86339200-86349200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:86340000-86357200	Weak transcription	Fetal Brain Female	brain
5	chr11:86341000-86347400	Weak transcription	Fetal Kidney	kidney
6	chr11:86341000-86349000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:86341000-86355400	Weak transcription	Adipose Nuclei	Adipose
8	chr11:86341600-86358800	Weak transcription	Brain Anterior Caudate	brain
9	chr11:86342000-86349200	Weak transcription	Fetal Heart	heart
10	chr11:86342200-86348400	Weak transcription	Left Ventricle	heart
11	chr11:86342200-86348400	Weak transcription	Right Ventricle	heart
12	chr11:86342200-86348800	Weak transcription	Brain Angular Gyrus	brain
13	chr11:86342200-86351400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:86342200-86353200	Weak transcription	Aorta	Aorta
15	chr11:86342200-86356400	Weak transcription	Fetal Stomach	stomach
16	chr11:86342600-86347400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:86343800-86350000	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:86344000-86373800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:86344200-86352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:86344400-86347000	Weak transcription	Ovary	ovary
21	chr11:86344400-86348400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:86344400-86349000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:86344600-86347000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:86344600-86347000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:86344600-86354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:86344800-86346600	Weak transcription	NH-A	brain
27	chr11:86344800-86346800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:86344800-86346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:86344800-86347000	Weak transcription	NHLF	lung
30	chr11:86344800-86347400	Weak transcription	HMEC	breast
31	chr11:86344800-86348800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:86344800-86349000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:86344800-86349000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:86344800-86349000	Weak transcription	NHEK	skin
35	chr11:86344800-86349000	Weak transcription	Osteobl	bone
36	chr11:86344800-86355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:86344800-86355800	Weak transcription	Pancreas	Pancrea
38	chr11:86345000-86346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:86345000-86346800	Weak transcription	HUVEC	blood vessel
40	chr11:86345000-86347800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:86345000-86348400	Weak transcription	Spleen	Spleen
42	chr11:86345000-86349400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:86345200-86346800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:86345200-86346800	Weak transcription	NHDF-Ad	bronchial
45	chr11:86345400-86346400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:86345400-86346600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:86345400-86353000	Weak transcription	HSMM	muscle
48	chr11:86345600-86346600	Weak transcription	A549	lung
49	chr11:86346000-86346400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:86346200-86346400	Enhancers	Gastric	stomach

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