Variant report

Variant	rs35487339
Chromosome Location	chr15:52273669-52273670
allele	-/A
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 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	chr15:52273590..52276860-chr15:52313793..52315606,3	MCF-7	breast:
5	chr15:52273097..52274841-chr15:52286884..52288398,2	K562	blood:
6	chr15:52267594..52270331-chr15:52272576..52274636,3	MCF-7	breast:
7	chr15:52272443..52274627-chr15:52305698..52308304,2	K562	blood:
8	chr15:52271637..52274025-chr15:52275587..52277212,2	MCF-7	breast:
9	chr15:52272323..52273861-chr15:52410160..52412706,2	MCF-7	breast:
10	chr15:52272236..52273812-chr15:52299761..52301744,2	K562	blood:
11	chr15:52273618..52277217-chr15:52282042..52285418,5	MCF-7	breast:
12	chr15:52272930..52275289-chr15:52472014..52473869,2	MCF-7	breast:
13	chr15:52271865..52274806-chr15:52313995..52316353,2	MCF-7	breast:
14	chr15:52273281..52276233-chr15:52432324..52433834,2	MCF-7	breast:
15	chr15:52272756..52275955-chr15:52369833..52372310,3	MCF-7	breast:
16	chr15:52269337..52272220-chr15:52273087..52274635,2	MCF-7	breast:
17	chr15:52272035..52276768-chr15:52309954..52313442,7	MCF-7	breast:

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1025185	0.84[AMR][1000 genomes]
rs16964657	0.81[AMR][1000 genomes]
rs17649820	0.86[AMR][1000 genomes]
rs17649826	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2162224	0.82[AMR][1000 genomes]
rs2250797	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2433219	0.83[AMR][1000 genomes]
rs2470592	0.87[AFR][1000 genomes]
rs2470606	0.81[AFR][1000 genomes]
rs2554317	0.87[AMR][1000 genomes]
rs2554323	0.82[AMR][1000 genomes]
rs2554338	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2570218	0.81[AMR][1000 genomes]
rs2570246	0.82[AMR][1000 genomes]
rs2570267	0.82[AMR][1000 genomes]
rs2570270	0.82[AMR][1000 genomes]
rs2570273	0.82[AMR][1000 genomes]
rs2570274	0.81[AMR][1000 genomes]
rs2593175	0.82[AMR][1000 genomes]
rs2593176	0.82[AMR][1000 genomes]
rs2593180	0.82[AMR][1000 genomes]
rs2593196	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2593197	0.89[AFR][1000 genomes]
rs2593203	0.81[AFR][1000 genomes]
rs2623257	0.82[AMR][1000 genomes]
rs2623277	0.82[AMR][1000 genomes]
rs2623278	0.82[AMR][1000 genomes]
rs2623287	0.82[AMR][1000 genomes]
rs2959297	0.92[AMR][1000 genomes]
rs3099570	0.92[AMR][1000 genomes]
rs4775990	0.81[AMR][1000 genomes]
rs59782457	0.83[AMR][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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52264600-52273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr15:52264600-52273800	Weak transcription	Brain Anterior Caudate	brain
3	chr15:52264600-52273800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:52264600-52273800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:52264600-52273800	Weak transcription	Brain Substantia Nigra	brain
6	chr15:52264600-52273800	Weak transcription	Thymus	Thymus
7	chr15:52264600-52274000	Weak transcription	Colonic Mucosa	Colon
8	chr15:52264600-52274200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:52264600-52274400	Weak transcription	Pancreas	Pancrea
10	chr15:52264800-52273800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:52264800-52273800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:52264800-52273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:52264800-52273800	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:52264800-52274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:52264800-52274000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:52265000-52273800	Weak transcription	HSMM	muscle
17	chr15:52265200-52273800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:52265200-52273800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:52265600-52273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:52266400-52273800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:52266600-52273800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:52267200-52273800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52270200-52273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52270600-52273800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:52271200-52274000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:52272600-52273800	Enhancers	HepG2	liver
27	chr15:52273000-52273800	Enhancers	Primary hematopoietic stem cells	blood
28	chr15:52273000-52273800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr15:52273000-52273800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:52273000-52273800	Enhancers	Liver	Liver
31	chr15:52273000-52273800	Enhancers	Duodenum Mucosa	Duodenum
32	chr15:52273000-52273800	Enhancers	Fetal Thymus	thymus
33	chr15:52273000-52273800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr15:52273000-52274000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr15:52273000-52274600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:52273200-52273800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:52273200-52273800	Enhancers	Adipose Nuclei	Adipose
38	chr15:52273200-52273800	Enhancers	Colon Smooth Muscle	Colon
39	chr15:52273200-52273800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr15:52273200-52273800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:52273200-52274600	Enhancers	Fetal Intestine Small	intestine
42	chr15:52273200-52275400	Flanking Active TSS	Dnd41	blood
43	chr15:52273400-52273800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:52273400-52273800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:52273400-52274600	Enhancers	Psoas Muscle	Psoas
46	chr15:52273400-52274600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr15:52273600-52273800	Enhancers	Primary T cells from cord blood	blood
48	chr15:52273600-52273800	Enhancers	Brain Hippocampus Middle	brain
49	chr15:52273600-52273800	Enhancers	A549	lung
50	chr15:52273600-52273800	Enhancers	HSMMtube	muscle

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