Variant report

Variant	rs2433220
Chromosome Location	chr15:52273449-52273450
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52272584..52276027-chr15:52308541..52312916,5	K562	blood:
2	chr15:52273041..52275862-chr15:52300749..52303075,2	MCF-7	breast:
3	chr15:52272788..52276993-chr15:52369760..52371998,4	MCF-7	breast:
4	chr15:52273097..52274841-chr15:52286884..52288398,2	K562	blood:
5	chr15:52267594..52270331-chr15:52272576..52274636,3	MCF-7	breast:
6	chr15:52272443..52274627-chr15:52305698..52308304,2	K562	blood:
7	chr15:52271637..52274025-chr15:52275587..52277212,2	MCF-7	breast:
8	chr15:52272323..52273861-chr15:52410160..52412706,2	MCF-7	breast:
9	chr15:52272236..52273812-chr15:52299761..52301744,2	K562	blood:
10	chr15:52272930..52275289-chr15:52472014..52473869,2	MCF-7	breast:
11	chr15:52271865..52274806-chr15:52313995..52316353,2	MCF-7	breast:
12	chr15:52273281..52276233-chr15:52432324..52433834,2	MCF-7	breast:
13	chr15:52272756..52275955-chr15:52369833..52372310,3	MCF-7	breast:
14	chr15:52269337..52272220-chr15:52273087..52274635,2	MCF-7	breast:
15	chr15:52272035..52276768-chr15:52309954..52313442,7	MCF-7	breast:
16	chr15:52271043..52273593-chr15:52500641..52502378,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1025184	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1035739	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11638677	0.80[EUR][1000 genomes]
rs12902346	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17612123	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2052706	0.80[EUR][1000 genomes]
rs2052709	0.80[EUR][1000 genomes]
rs2241503	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2251135	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2252606	0.80[EUR][1000 genomes]
rs2253116	0.81[EUR][1000 genomes]
rs2414122	0.80[EUR][1000 genomes]
rs2433222	0.80[EUR][1000 genomes]
rs2436657	0.80[EUR][1000 genomes]
rs2436658	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2448953	0.80[EUR][1000 genomes]
rs2470590	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470591	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2470602	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2470603	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2470604	0.82[AMR][1000 genomes]
rs2470605	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2470607	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2470612	0.80[EUR][1000 genomes]
rs2470616	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2554337	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2554342	0.81[EUR][1000 genomes]
rs2554349	0.80[EUR][1000 genomes]
rs2554350	0.80[EUR][1000 genomes]
rs2570263	0.80[EUR][1000 genomes]
rs2570268	0.81[EUR][1000 genomes]
rs2570269	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2570271	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2570275	0.82[EUR][1000 genomes]
rs2593168	0.80[EUR][1000 genomes]
rs2593173	0.80[EUR][1000 genomes]
rs2593182	0.80[EUR][1000 genomes]
rs2593183	0.80[EUR][1000 genomes]
rs2593185	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2593187	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2593188	0.82[EUR][1000 genomes]
rs2593194	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593198	0.82[EUR][1000 genomes]
rs2593199	0.82[EUR][1000 genomes]
rs2593202	0.82[EUR][1000 genomes]
rs2593204	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2623243	0.82[EUR][1000 genomes]
rs2623244	0.82[EUR][1000 genomes]
rs2623255	0.81[EUR][1000 genomes]
rs2623266	0.80[EUR][1000 genomes]
rs2623279	0.80[EUR][1000 genomes]
rs2623282	0.80[EUR][1000 genomes]
rs2623283	0.80[EUR][1000 genomes]
rs2623284	0.80[EUR][1000 genomes]
rs2623285	0.80[EUR][1000 genomes]
rs2623286	0.80[EUR][1000 genomes]
rs2623288	0.81[EUR][1000 genomes]
rs2623289	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2912188	0.80[EUR][1000 genomes]
rs2912190	0.91[EUR][1000 genomes]
rs2921957	0.87[EUR][1000 genomes]
rs2929422	0.80[EUR][1000 genomes]
rs2959291	0.80[EUR][1000 genomes]
rs2959292	0.80[EUR][1000 genomes]
rs2959293	0.80[EUR][1000 genomes]
rs2959302	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3110551	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3110553	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34842090	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59808035	0.88[ASN][1000 genomes]
rs62015190	0.82[EUR][1000 genomes]
rs7162554	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029036	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs990665	0.80[EUR][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	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv569421	chr15:52268144-52282436	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52264600-52273600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:52264600-52273600	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:52264600-52273600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:52264600-52273600	Weak transcription	Stomach Mucosa	stomach
5	chr15:52264600-52273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:52264600-52273800	Weak transcription	Brain Anterior Caudate	brain
7	chr15:52264600-52273800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:52264600-52273800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:52264600-52273800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:52264600-52273800	Weak transcription	Thymus	Thymus
11	chr15:52264600-52274000	Weak transcription	Colonic Mucosa	Colon
12	chr15:52264600-52274200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:52264600-52274400	Weak transcription	Pancreas	Pancrea
14	chr15:52264800-52273600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:52264800-52273600	Weak transcription	NHEK	skin
16	chr15:52264800-52273800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:52264800-52273800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:52264800-52273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:52264800-52273800	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:52264800-52274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:52264800-52274000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:52265000-52273800	Weak transcription	HSMM	muscle
23	chr15:52265200-52273800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:52265200-52273800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:52265600-52273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:52266400-52273800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:52266600-52273800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:52267200-52273800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:52270200-52273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:52270600-52273800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:52271200-52274000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:52272600-52273800	Enhancers	HepG2	liver
33	chr15:52272800-52273600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:52273000-52273600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:52273000-52273600	Enhancers	Right Ventricle	heart
36	chr15:52273000-52273600	Enhancers	Hela-S3	cervix
37	chr15:52273000-52273800	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:52273000-52273800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:52273000-52273800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:52273000-52273800	Enhancers	Liver	Liver
41	chr15:52273000-52273800	Enhancers	Duodenum Mucosa	Duodenum
42	chr15:52273000-52273800	Enhancers	Fetal Thymus	thymus
43	chr15:52273000-52273800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr15:52273000-52274000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr15:52273000-52274600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:52273200-52273600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:52273200-52273600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr15:52273200-52273800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:52273200-52273800	Enhancers	Adipose Nuclei	Adipose
50	chr15:52273200-52273800	Enhancers	Colon Smooth Muscle	Colon

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