Variant report

Variant	rs17238859
Chromosome Location	chr15:56957179-56957180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56954012..56957476-chr15:56973562..56976021,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10518872	0.82[EUR][1000 genomes]
rs1087705	0.82[EUR][1000 genomes]
rs11071285	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438728	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439116	0.89[EUR][1000 genomes]
rs12439563	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439586	0.82[EUR][1000 genomes]
rs12440006	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441746	0.84[EUR][1000 genomes]
rs12443178	0.89[EUR][1000 genomes]
rs12903143	0.89[EUR][1000 genomes]
rs12907983	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1564557	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1600829	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1600831	0.84[EUR][1000 genomes]
rs17238880	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17819562	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17819592	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1834199	0.89[EUR][1000 genomes]
rs2052641	0.89[EUR][1000 genomes]
rs2161935	0.82[EUR][1000 genomes]
rs2170462	0.82[EUR][1000 genomes]
rs2459565	0.82[EUR][1000 genomes]
rs2676178	0.82[EUR][1000 genomes]
rs2676181	0.82[EUR][1000 genomes]
rs2899599	0.82[EUR][1000 genomes]
rs4287503	0.89[EUR][1000 genomes]
rs4774885	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs480701	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493888	0.89[EUR][1000 genomes]
rs7176472	0.82[EUR][1000 genomes]
rs74015901	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
2	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:56917800-56990600	Weak transcription	NHLF	lung
5	chr15:56918400-56957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
7	chr15:56922000-56958000	Weak transcription	Lung	lung
8	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:56924000-56990800	Weak transcription	NHEK	skin
10	chr15:56924600-56957200	Weak transcription	HUVEC	blood vessel
11	chr15:56928400-56996800	Weak transcription	Gastric	stomach
12	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
13	chr15:56938600-56968200	Weak transcription	HMEC	breast
14	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
16	chr15:56941400-56960200	Weak transcription	Spleen	Spleen
17	chr15:56943600-56958000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:56944200-56959600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:56944400-56957600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:56944600-56964600	Weak transcription	K562	blood
21	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
26	chr15:56946000-56957800	Weak transcription	Fetal Intestine Small	intestine
27	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:56946200-56957400	Weak transcription	GM12878-XiMat	blood
29	chr15:56946200-56971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
31	chr15:56947000-56960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:56948200-56961400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:56950200-56969200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:56950400-56965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:56950600-56967200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:56951800-56960800	Strong transcription	Adipose Nuclei	Adipose
37	chr15:56952400-56960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:56952800-56960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:56953000-56958600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:56953000-56960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:56953200-56959000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:56953200-56959800	Strong transcription	Liver	Liver
43	chr15:56953200-56961600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:56953800-56960000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:56954000-56959200	Strong transcription	Placenta	Placenta
46	chr15:56954000-56968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:56954200-56965200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:56954400-56960400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:56954400-56960600	Strong transcription	Osteobl	bone
50	chr15:56954600-56960400	Strong transcription	Primary B cells from peripheral blood	blood

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