Variant report

Variant	rs28699115
Chromosome Location	chr15:52030020-52030021
allele	G/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52029378..52032499-chr15:52121077..52123299,3	MCF-7	breast:
2	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
3	chr15:52005662..52007756-chr15:52028876..52031424,2	MCF-7	breast:
4	chr15:52029435..52031649-chr15:52311154..52313570,2	K562	blood:
5	chr15:51914058..51915723-chr15:52028393..52030272,2	MCF-7	breast:
6	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
7	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
8	chr15:51911576..51916583-chr15:52027382..52031699,5	MCF-7	breast:
9	chr12:64614231..64616104-chr15:52029344..52031052,2	MCF-7	breast:
10	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259377	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000174206	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000259296	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1001690	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10444824	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10444825	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070865	0.97[EUR][1000 genomes]
rs11070866	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070867	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070868	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070869	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630579	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630943	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631858	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636869	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11637876	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12050524	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903500	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904413	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904900	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905283	0.83[EUR][1000 genomes]
rs12912928	0.83[EUR][1000 genomes]
rs12913583	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17526463	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17610862	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17611193	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1840708	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863430	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2010026	0.90[EUR][1000 genomes]
rs2034856	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554314	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2929426	0.80[ASN][1000 genomes]
rs3088312	0.96[EUR][1000 genomes]
rs34098740	0.85[ASN][1000 genomes]
rs34504520	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35270232	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35391204	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35823585	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794532	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3898905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4365237	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55887408	0.88[AMR][1000 genomes]
rs56148956	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56185947	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493520	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493521	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493525	0.82[EUR][1000 genomes]
rs6493526	0.82[EUR][1000 genomes]
rs7162176	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164961	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7166962	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7168659	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7170091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170910	0.81[EUR][1000 genomes]
rs7171516	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171796	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174497	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7174808	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175017	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178166	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178561	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7178776	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7178940	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7179599	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181540	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726158	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8024585	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8025069	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026521	0.84[EUR][1000 genomes]
rs8028486	0.84[EUR][1000 genomes]
rs8028922	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033433	0.82[EUR][1000 genomes]
rs8035126	0.81[EUR][1000 genomes]
rs8035173	0.87[EUR][1000 genomes]
rs8040975	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040986	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944235	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	esv3322785	chr15:52028185-52031033	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
3	esv3433188	chr15:52028510-52031058	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52027000-52030400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:52028400-52030200	Active TSS	Fetal Brain Female	brain
3	chr15:52028400-52030200	Active TSS	GM12878-XiMat	blood
4	chr15:52028600-52030200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:52028600-52030400	Active TSS	Fetal Intestine Small	intestine
6	chr15:52028600-52030400	Active TSS	Right Atrium	heart
7	chr15:52028800-52030200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr15:52028800-52030200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:52028800-52030200	Active TSS	Left Ventricle	heart
10	chr15:52028800-52030200	Active TSS	Psoas Muscle	Psoas
11	chr15:52028800-52030200	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr15:52028800-52030400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr15:52028800-52030400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:52028800-52030400	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr15:52028800-52030400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr15:52028800-52030400	Active TSS	Lung	lung
17	chr15:52028800-52030400	Active TSS	Ovary	ovary
18	chr15:52028800-52030600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr15:52028800-52030600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr15:52029000-52030200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:52029000-52030200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:52029000-52030200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr15:52029000-52030200	Active TSS	Primary B cells from peripheral blood	blood
24	chr15:52029000-52030200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr15:52029000-52030200	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr15:52029000-52030200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:52029000-52030200	Active TSS	Brain Angular Gyrus	brain
28	chr15:52029000-52030200	Active TSS	Brain Substantia Nigra	brain
29	chr15:52029000-52030200	Active TSS	Esophagus	oesophagus
30	chr15:52029000-52030200	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr15:52029000-52030400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:52029000-52030400	Active TSS	Brain Hippocampus Middle	brain
33	chr15:52029000-52030400	Active TSS	Colon Smooth Muscle	Colon
34	chr15:52029000-52030400	Active TSS	Small Intestine	intestine
35	chr15:52029000-52030400	Active TSS	HSMM	muscle
36	chr15:52029000-52030600	Active TSS	Aorta	Aorta
37	chr15:52029200-52030200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr15:52029200-52030200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr15:52029200-52030200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr15:52029200-52030200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:52029200-52030200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:52029200-52030200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:52029200-52030200	Active TSS	Primary T cells from cord blood	blood
44	chr15:52029200-52030200	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr15:52029200-52030200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:52029200-52030200	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:52029200-52030200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr15:52029200-52030200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr15:52029200-52030200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:52029200-52030200	Active TSS	Cortex derived primary cultured neurospheres	brain

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