Variant report

Variant	rs17649826
Chromosome Location	chr15:52273823-52273824
allele	C/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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52273697..52275326-chr15:52431024..52433889,2	MCF-7	breast:
2	chr15:52272584..52276027-chr15:52308541..52312916,5	K562	blood:
3	chr15:52273041..52275862-chr15:52300749..52303075,2	MCF-7	breast:
4	chr15:52273823..52274921-chr15:52431326..52432805,7	MCF-7	breast:
5	chr15:52272788..52276993-chr15:52369760..52371998,4	MCF-7	breast:
6	chr15:52273590..52276860-chr15:52313793..52315606,3	MCF-7	breast:
7	chr15:52273097..52274841-chr15:52286884..52288398,2	K562	blood:
8	chr15:52267594..52270331-chr15:52272576..52274636,3	MCF-7	breast:
9	chr15:52272443..52274627-chr15:52305698..52308304,2	K562	blood:
10	chr15:52271637..52274025-chr15:52275587..52277212,2	MCF-7	breast:
11	chr15:52272323..52273861-chr15:52410160..52412706,2	MCF-7	breast:
12	chr15:52273618..52277217-chr15:52282042..52285418,5	MCF-7	breast:
13	chr15:52273761..52275142-chr15:52431751..52433231,16	MCF-7	breast:
14	chr15:52272930..52275289-chr15:52472014..52473869,2	MCF-7	breast:
15	chr15:52273740..52275990-chr15:52310375..52312571,2	K562	blood:
16	chr15:52271865..52274806-chr15:52313995..52316353,2	MCF-7	breast:
17	chr15:52273281..52276233-chr15:52432324..52433834,2	MCF-7	breast:
18	chr15:52272756..52275955-chr15:52369833..52372310,3	MCF-7	breast:
19	chr15:52269337..52272220-chr15:52273087..52274635,2	MCF-7	breast:
20	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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1025185	0.97[AMR][1000 genomes]
rs10519323	1.00[AFR][1000 genomes]
rs12438469	1.00[AFR][1000 genomes]
rs17649178	1.00[AFR][1000 genomes]
rs17649255	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17649692	0.85[AMR][1000 genomes]
rs17649801	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17649820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17706076	0.85[AMR][1000 genomes]
rs2052707	0.85[AMR][1000 genomes]
rs2250797	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2554338	0.95[ASN][1000 genomes]
rs2593196	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2959297	0.84[AMR][1000 genomes]
rs3099570	0.84[AMR][1000 genomes]
rs34407523	1.00[AFR][1000 genomes]
rs35487339	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4775989	0.91[AMR][1000 genomes]
rs4775990	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166322	0.85[AMR][1000 genomes]
rs7170429	0.88[AMR][1000 genomes]
rs7170700	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8042310	1.00[AFR][1000 genomes];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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52264600-52274000	Weak transcription	Colonic Mucosa	Colon
2	chr15:52264600-52274200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:52264600-52274400	Weak transcription	Pancreas	Pancrea
4	chr15:52264800-52274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:52264800-52274000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:52271200-52274000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:52273000-52274000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr15:52273000-52274600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:52273200-52274600	Enhancers	Fetal Intestine Small	intestine
10	chr15:52273200-52275400	Flanking Active TSS	Dnd41	blood
11	chr15:52273400-52274600	Enhancers	Psoas Muscle	Psoas
12	chr15:52273400-52274600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr15:52273600-52274000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr15:52273600-52274000	Enhancers	HMEC	breast
15	chr15:52273600-52274200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr15:52273600-52274200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:52273600-52274400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:52273600-52274400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:52273600-52274600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr15:52273600-52274600	Flanking Active TSS	Hela-S3	cervix
21	chr15:52273600-52274800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:52273600-52274800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:52273600-52274800	Enhancers	Stomach Mucosa	stomach
24	chr15:52273800-52274000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:52273800-52274000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:52273800-52274000	Enhancers	Primary B cells from cord blood	blood
27	chr15:52273800-52274000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr15:52273800-52274000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr15:52273800-52274000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:52273800-52274000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:52273800-52274000	Flanking Active TSS	Fetal Thymus	thymus
32	chr15:52273800-52274000	Enhancers	Rectal Smooth Muscle	rectum
33	chr15:52273800-52274000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr15:52273800-52274000	Flanking Active TSS	Thymus	Thymus
35	chr15:52273800-52274000	Flanking Active TSS	HSMMtube	muscle
36	chr15:52273800-52274000	Active TSS	NHLF	lung
37	chr15:52273800-52274200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:52273800-52274200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:52273800-52274200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:52273800-52274200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52273800-52274200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:52273800-52274200	Enhancers	Brain Substantia Nigra	brain
43	chr15:52273800-52274200	Active TSS	GM12878-XiMat	blood
44	chr15:52273800-52274200	Active TSS	HSMM	muscle
45	chr15:52273800-52274400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:52273800-52274400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:52273800-52274400	Enhancers	Brain Angular Gyrus	brain
48	chr15:52273800-52274400	Active TSS	Fetal Kidney	kidney
49	chr15:52273800-52274400	Active TSS	Right Atrium	heart
50	chr15:52273800-52274600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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