Variant report

Variant	rs28565228
Chromosome Location	chr15:40498172-40498173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40398197..40401175-chr15:40497196..40499057,2	MCF-7	breast:
2	chr15:40490264..40493661-chr15:40497414..40500104,3	MCF-7	breast:
3	chr15:40487922..40490370-chr15:40496350..40498700,2	K562	blood:
4	chr15:40491881..40494324-chr15:40495834..40498755,2	K562	blood:

Variant related genes	Relation type
ENSG00000156970	Chromatin interaction
ENSG00000104081	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11070254	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070255	1.00[EUR][1000 genomes]
rs12102172	1.00[EUR][1000 genomes]
rs12385956	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380113	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380241	1.00[EUR][1000 genomes]
rs1494534	1.00[EUR][1000 genomes]
rs1801528	1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs28390245	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28417868	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28418337	1.00[AMR][1000 genomes]
rs28485685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501335	1.00[EUR][1000 genomes]
rs28526743	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28561898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28606396	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637656	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637697	1.00[EUR][1000 genomes]
rs28657938	1.00[EUR][1000 genomes]
rs28668026	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673302	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28744626	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28750294	1.00[EUR][1000 genomes]
rs28792493	1.00[EUR][1000 genomes]
rs28844897	1.00[EUR][1000 genomes]
rs28869227	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35611758	1.00[EUR][1000 genomes]
rs55984256	1.00[EUR][1000 genomes]
rs56010221	1.00[EUR][1000 genomes]
rs56888636	1.00[EUR][1000 genomes]
rs57029027	1.00[EUR][1000 genomes]
rs58216655	1.00[EUR][1000 genomes]
rs58355728	1.00[AMR][1000 genomes]
rs58584688	1.00[EUR][1000 genomes]
rs58870954	1.00[EUR][1000 genomes]
rs60743501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60889301	1.00[EUR][1000 genomes]
rs61579851	1.00[EUR][1000 genomes]
rs61678895	1.00[EUR][1000 genomes]
rs6492943	1.00[EUR][1000 genomes]
rs7164281	1.00[EUR][1000 genomes]
rs7168394	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168416	1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7175153	1.00[EUR][1000 genomes]
rs7178873	1.00[EUR][1000 genomes]
rs73377835	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383123	1.00[EUR][1000 genomes]
rs73383129	1.00[EUR][1000 genomes]
rs73385108	1.00[EUR][1000 genomes]
rs73385110	1.00[EUR][1000 genomes]
rs73389487	1.00[EUR][1000 genomes]
rs73389489	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389492	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389507	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389520	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389531	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389536	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390146	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390155	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390162	1.00[EUR][1000 genomes]
rs73390167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390168	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390187	1.00[EUR][1000 genomes]
rs73391309	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73391316	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73392641	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8026988	1.00[EUR][1000 genomes]
rs8039298	1.00[EUR][1000 genomes]
rs8364	1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs967945	1.00[AMR][1000 genomes]
rs9806126	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806144	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40454600-40502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
6	chr15:40455600-40518200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:40455600-40522200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
9	chr15:40456200-40524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:40456200-40524000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40471400-40517600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:40471400-40524400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40473200-40517800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:40473600-40525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:40475000-40526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:40475400-40522600	Strong transcription	Dnd41	blood
17	chr15:40480600-40500000	Weak transcription	Fetal Intestine Small	intestine
18	chr15:40481800-40524400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:40483000-40526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:40483200-40501000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:40483800-40509400	Weak transcription	Fetal Brain Male	brain
22	chr15:40485400-40513800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:40485400-40527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40486600-40521000	Weak transcription	Placenta	Placenta
25	chr15:40487600-40518200	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr15:40487800-40509400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:40488200-40517000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr15:40488800-40506800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:40489800-40502000	Weak transcription	Colonic Mucosa	Colon
30	chr15:40490000-40498600	Weak transcription	Fetal Lung	lung
31	chr15:40490400-40507000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:40490600-40506800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:40490800-40519000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:40491000-40526600	Weak transcription	Primary B cells from cord blood	blood
35	chr15:40491200-40507600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:40491200-40527200	Strong transcription	Fetal Thymus	thymus
37	chr15:40491400-40505200	Weak transcription	Primary T cells from cord blood	blood
38	chr15:40491600-40524600	Weak transcription	Fetal Heart	heart
39	chr15:40491800-40523200	Weak transcription	Esophagus	oesophagus
40	chr15:40492000-40498400	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:40492600-40498600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:40492800-40498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:40492800-40498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:40492800-40498400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:40492800-40498400	Weak transcription	Thymus	Thymus
46	chr15:40492800-40498400	Weak transcription	NHEK	skin
47	chr15:40492800-40498400	Weak transcription	NHLF	lung
48	chr15:40492800-40498600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:40492800-40509400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:40492800-40524000	Weak transcription	Fetal Kidney	kidney

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