Variant report

Variant	rs28610479
Chromosome Location	chr15:59392105-59392106
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59391505..59393672-chr15:59394009..59396903,2	MCF-7	breast:
2	chr15:59388228..59393746-chr15:59399093..59403821,6	K562	blood:
3	chr15:59390265..59393691-chr15:59395315..59398621,4	K562	blood:

Variant related genes	Relation type
ENSG00000157456	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10431762	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431791	0.84[ASN][1000 genomes]
rs10431792	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518996	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1074701	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1074702	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851642	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10851643	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11539756	0.90[AMR][1000 genomes]
rs11635820	0.84[ASN][1000 genomes]
rs11852461	0.83[ASN][1000 genomes]
rs11853828	0.81[AMR][1000 genomes]
rs12101733	0.82[ASN][1000 genomes]
rs12437587	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438111	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438208	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438962	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12440692	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441973	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12442086	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12442134	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12442301	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12900369	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902628	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906212	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12907187	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907277	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910987	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912429	0.81[ASN][1000 genomes]
rs12913177	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915899	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12917373	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1345116	0.82[ASN][1000 genomes]
rs1374156	0.85[ASN][1000 genomes]
rs1446239	0.83[ASN][1000 genomes]
rs1665050	0.81[ASN][1000 genomes]
rs16940998	0.86[ASN][1000 genomes]
rs16941014	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17236369	0.83[ASN][1000 genomes]
rs17236453	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17302163	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1809588	0.80[ASN][1000 genomes]
rs1867757	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1971181	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2121236	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2121237	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289895	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2414619	0.86[ASN][1000 genomes]
rs28391430	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514475	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899640	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34338282	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34407560	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34718679	0.85[ASN][1000 genomes]
rs34859729	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34977427	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35066133	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35168204	0.84[AMR][1000 genomes]
rs35204615	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35460138	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35555888	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769647	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36125140	0.80[ASN][1000 genomes]
rs3794501	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4531679	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774321	0.87[ASN][1000 genomes]
rs4775110	0.82[ASN][1000 genomes]
rs4775111	0.87[ASN][1000 genomes]
rs4775114	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775115	0.81[ASN][1000 genomes]
rs57361749	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58087223	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58335303	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58417366	0.83[ASN][1000 genomes]
rs59282449	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59514650	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60262196	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60741546	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62002516	0.86[ASN][1000 genomes]
rs62002543	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62002544	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62004080	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6494054	0.85[ASN][1000 genomes]
rs6494064	0.86[ASN][1000 genomes]
rs6494065	0.82[ASN][1000 genomes]
rs6494069	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480503	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165028	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165817	0.90[ASN][1000 genomes]
rs7168102	0.82[ASN][1000 genomes]
rs7173135	0.84[ASN][1000 genomes]
rs7175215	0.81[ASN][1000 genomes]
rs7175246	0.85[ASN][1000 genomes]
rs7176281	0.84[ASN][1000 genomes]
rs7176576	0.85[ASN][1000 genomes]
rs7178935	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73418863	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73418864	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755786	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8025246	0.83[ASN][1000 genomes]
rs8026611	0.84[ASN][1000 genomes]
rs8027536	0.83[ASN][1000 genomes]
rs8028764	0.85[ASN][1000 genomes]
rs8029336	0.81[ASN][1000 genomes]
rs8036907	0.83[AMR][1000 genomes]
rs8037569	0.85[ASN][1000 genomes]
rs8040456	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041221	0.86[ASN][1000 genomes]
rs8041704	0.81[ASN][1000 genomes]
rs8042516	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042896	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs877269	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9302206	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59344400-59392800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:59354400-59396800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:59355400-59392800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:59355600-59392800	Strong transcription	Liver	Liver
5	chr15:59355600-59396600	Weak transcription	Fetal Heart	heart
6	chr15:59359400-59396600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:59364800-59392600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:59368200-59392800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:59371600-59392800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:59374000-59396800	Weak transcription	Ovary	ovary
11	chr15:59374200-59396600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:59374200-59396800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:59374200-59396800	Weak transcription	Right Ventricle	heart
14	chr15:59374400-59396800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:59377200-59397000	Weak transcription	Gastric	stomach
16	chr15:59379400-59396600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:59380800-59392800	Strong transcription	A549	lung
18	chr15:59384200-59396400	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:59384200-59396600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:59384200-59396600	Weak transcription	NHLF	lung
21	chr15:59384200-59396800	Weak transcription	Lung	lung
22	chr15:59384200-59396800	Weak transcription	Pancreas	Pancrea
23	chr15:59384800-59396400	Weak transcription	K562	blood
24	chr15:59385200-59392200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:59385200-59396800	Weak transcription	Psoas Muscle	Psoas
26	chr15:59385200-59396800	Weak transcription	Small Intestine	intestine
27	chr15:59385400-59396400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:59385400-59396600	Weak transcription	Brain Angular Gyrus	brain
29	chr15:59385400-59396600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:59385400-59396800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:59385400-59396800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:59385400-59396800	Weak transcription	Brain Germinal Matrix	brain
33	chr15:59385800-59396600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:59385800-59396800	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:59385800-59397000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:59385800-59397400	Weak transcription	Spleen	Spleen
37	chr15:59386600-59396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:59387200-59396800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:59387400-59396600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr15:59387400-59396800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:59387800-59396400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:59387800-59396600	Weak transcription	NHEK	skin
43	chr15:59388000-59396400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:59388400-59396600	Weak transcription	Fetal Kidney	kidney
45	chr15:59388800-59396600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:59389200-59392200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:59389200-59392200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:59389200-59392200	Weak transcription	Fetal Brain Female	brain
49	chr15:59389200-59392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:59389200-59392400	Weak transcription	HSMMtube	muscle

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