Variant report

Variant	rs2570251
Chromosome Location	chr15:52155314-52155315
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	chr15:52120607..52125174-chr15:52151783..52155506,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10444798	0.86[EUR][1000 genomes]
rs10444823	0.95[EUR][1000 genomes]
rs10775145	0.94[EUR][1000 genomes]
rs11070864	0.83[EUR][1000 genomes]
rs1135871	0.80[ASN][1000 genomes]
rs11630084	0.83[EUR][1000 genomes]
rs11632106	0.81[EUR][1000 genomes]
rs11636345	0.91[EUR][1000 genomes]
rs11638161	0.90[EUR][1000 genomes]
rs11638766	0.87[EUR][1000 genomes]
rs11638820	0.87[EUR][1000 genomes]
rs12903707	0.96[EUR][1000 genomes]
rs12917133	0.91[EUR][1000 genomes]
rs1350174	0.83[EUR][1000 genomes]
rs1545602	0.88[EUR][1000 genomes]
rs1811326	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1867984	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1902430	0.83[EUR][1000 genomes]
rs1972689	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2006772	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2006773	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2011995	0.80[AFR][1000 genomes]
rs2014638	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034857	0.91[EUR][1000 genomes]
rs2034858	0.91[EUR][1000 genomes]
rs2052705	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2052706	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2052709	0.84[AMR][1000 genomes]
rs2077743	0.83[EUR][1000 genomes]
rs2252606	0.81[AMR][1000 genomes]
rs2252831	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253116	0.84[AMR][1000 genomes]
rs2264339	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2303443	0.95[EUR][1000 genomes]
rs2414117	0.83[EUR][1000 genomes]
rs2414119	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2433222	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2436657	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2436661	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2436662	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470619	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2554305	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2554306	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2554307	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2554308	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2554322	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2554327	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2554328	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2554332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2554334	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2554336	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2554342	0.82[AMR][1000 genomes]
rs2554345	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2554348	0.86[AFR][1000 genomes]
rs2554349	0.88[AMR][1000 genomes]
rs2554350	0.88[AMR][1000 genomes]
rs2554353	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2570224	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570228	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2570231	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2570233	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2570235	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570236	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570237	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2570238	0.92[AMR][1000 genomes]
rs2570239	0.99[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2570240	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2570241	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2570248	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2570252	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570258	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2570260	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2570268	0.84[AMR][1000 genomes]
rs2570269	0.82[AMR][1000 genomes]
rs2570271	0.80[AMR][1000 genomes]
rs2570275	0.82[AMR][1000 genomes]
rs2593167	0.85[EUR][1000 genomes]
rs2593168	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2593170	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2593173	0.88[AMR][1000 genomes]
rs2593177	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2593179	0.80[AMR][1000 genomes]
rs2593182	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2593183	0.88[AMR][1000 genomes]
rs2593185	0.82[AMR][1000 genomes]
rs2593187	0.80[AMR][1000 genomes]
rs2593188	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2593191	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2593198	0.82[AMR][1000 genomes]
rs2593199	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2593202	0.82[AMR][1000 genomes]
rs2623243	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2623244	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2623254	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2623255	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2623259	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2623262	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623266	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2623271	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623279	0.84[AMR][1000 genomes]
rs2623281	0.84[AMR][1000 genomes]
rs2623282	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2623283	0.84[AMR][1000 genomes]
rs2623284	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2623285	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2623286	0.84[AMR][1000 genomes]
rs2623288	0.84[AMR][1000 genomes]
rs2623289	0.83[AMR][1000 genomes]
rs3751596	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794530	0.87[EUR][1000 genomes]
rs3794534	0.96[EUR][1000 genomes]
rs3794535	0.96[EUR][1000 genomes]
rs3794536	0.96[EUR][1000 genomes]
rs4238383	0.87[EUR][1000 genomes]
rs4502160	0.87[EUR][1000 genomes]
rs4534783	0.91[EUR][1000 genomes]
rs4622456	0.83[EUR][1000 genomes]
rs4774602	0.91[EUR][1000 genomes]
rs4775978	0.91[EUR][1000 genomes]
rs4775982	0.96[EUR][1000 genomes]
rs4775983	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55843525	0.84[EUR][1000 genomes]
rs55887408	0.91[EUR][1000 genomes]
rs6493518	0.87[EUR][1000 genomes]
rs6493519	0.91[EUR][1000 genomes]
rs6493522	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493523	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67895020	0.95[EUR][1000 genomes]
rs689884	0.87[EUR][1000 genomes]
rs7162554	0.82[AMR][1000 genomes]
rs7163176	0.83[EUR][1000 genomes]
rs7165585	0.83[EUR][1000 genomes]
rs7166110	0.86[EUR][1000 genomes]
rs7171459	0.96[EUR][1000 genomes]
rs7173375	0.83[EUR][1000 genomes]
rs7174941	0.94[EUR][1000 genomes]
rs7181553	0.85[EUR][1000 genomes]
rs7182917	0.91[EUR][1000 genomes]
rs8024081	0.91[EUR][1000 genomes]
rs8024088	0.91[EUR][1000 genomes]
rs8024589	0.91[EUR][1000 genomes]
rs8028258	0.83[EUR][1000 genomes]
rs8028890	0.90[EUR][1000 genomes]
rs8031045	0.91[ASN][1000 genomes]
rs8040991	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041268	0.96[EUR][1000 genomes]
rs919059	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs990665	0.90[AMR][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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:52139400-52156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:52140200-52155400	Weak transcription	HSMMtube	muscle
4	chr15:52140600-52155400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:52141400-52155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
7	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:52142200-52155400	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:52145000-52156600	Weak transcription	Fetal Brain Female	brain
10	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
11	chr15:52148200-52157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:52149000-52161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:52149200-52155400	Weak transcription	Ovary	ovary
15	chr15:52149200-52156200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:52149400-52156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
18	chr15:52149600-52155600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:52149600-52156800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:52149800-52156400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:52149800-52156400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:52149800-52156400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:52149800-52160600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:52149800-52168000	Weak transcription	Right Ventricle	heart
25	chr15:52150600-52160800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:52151600-52155400	Weak transcription	Thymus	Thymus
27	chr15:52151800-52156400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:52152200-52156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:52152400-52170000	Weak transcription	Pancreas	Pancrea
30	chr15:52152400-52170800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:52153200-52156800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:52153200-52158400	Genic enhancers	A549	lung
33	chr15:52153200-52161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:52153200-52161600	Genic enhancers	NHEK	skin
35	chr15:52153400-52155800	Weak transcription	Colonic Mucosa	Colon
36	chr15:52153400-52156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:52153400-52157000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:52153400-52158400	Strong transcription	Hela-S3	cervix
39	chr15:52153400-52161600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:52153600-52155400	Weak transcription	Fetal Kidney	kidney
41	chr15:52153800-52158000	Strong transcription	GM12878-XiMat	blood
42	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
43	chr15:52154000-52156200	Weak transcription	Gastric	stomach
44	chr15:52154000-52161600	Genic enhancers	HMEC	breast
45	chr15:52154200-52155400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr15:52154200-52156200	Weak transcription	Esophagus	oesophagus
47	chr15:52154400-52155400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:52154400-52155400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:52154400-52155600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr15:52154400-52159400	Weak transcription	Fetal Heart	heart

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