Variant report

Variant	rs16945588
Chromosome Location	chr15:45906996-45906997
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45750663..45751216-chr15:45906499..45907103,2	MCF-7	breast:
2	chr15:45722770..45723742-chr15:45906160..45907111,2	MCF-7	breast:
3	chr15:45750024..45753283-chr15:45906121..45908328,3	K562	blood:
4	chr15:45722138..45723083-chr15:45906168..45907021,2	MCF-7	breast:
5	chr15:45749857..45751632-chr15:45906009..45907129,10	K562	blood:
6	chr15:45748656..45751923-chr15:45905497..45908734,4	K562	blood:
7	chr15:45749851..45751603-chr15:45905582..45907231,11	MCF-7	breast:
8	chr15:45884792..45886658-chr15:45905385..45908007,2	MCF-7	breast:
9	chr15:45722080..45723112-chr15:45906107..45907094,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166920	Chromatin interaction
ENSG00000259354	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152775	0.93[AMR][1000 genomes]
rs10152792	0.93[AMR][1000 genomes]
rs1153841	1.00[MEX][hapmap]
rs1288849	1.00[MEX][hapmap]
rs13376	0.82[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes]
rs1442797	0.88[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs1529353	0.93[AMR][1000 genomes]
rs1529354	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs1547488	1.00[MEX][hapmap]
rs1547489	1.00[MEX][hapmap]
rs1547490	1.00[MEX][hapmap]
rs1559892	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs1629871	1.00[MEX][hapmap]
rs16944196	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs16944305	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs16945605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1970374	0.93[AMR][1000 genomes]
rs2412958	0.85[AMR][1000 genomes]
rs2467874	1.00[MEX][hapmap]
rs2467875	1.00[MEX][hapmap]
rs3858908	0.93[AMR][1000 genomes]
rs4598849	0.90[AFR][1000 genomes]
rs57263027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60561729	0.93[AMR][1000 genomes]
rs61169737	0.93[AMR][1000 genomes]
rs61756712	0.93[AMR][1000 genomes]
rs6493153	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs679569	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7163098	0.86[AMR][1000 genomes]
rs7165846	0.93[AMR][1000 genomes]
rs7166434	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs7168672	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs7170941	0.93[AMR][1000 genomes]
rs7173046	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs7183382	0.82[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes]
rs719018	1.00[MEX][hapmap];0.82[YRI][hapmap]
rs719019	0.88[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs73412479	0.85[AMR][1000 genomes]
rs73412484	0.85[AMR][1000 genomes]
rs73412488	0.85[AMR][1000 genomes]
rs73412490	0.85[AMR][1000 genomes]
rs73414454	0.85[AMR][1000 genomes]
rs73414486	0.93[AMR][1000 genomes]
rs73416403	0.93[AMR][1000 genomes]
rs73416407	0.93[AMR][1000 genomes]
rs73416479	0.93[AMR][1000 genomes]
rs73416487	0.93[AMR][1000 genomes]
rs73420456	0.93[AMR][1000 genomes]
rs7342662	0.88[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs7495403	0.93[AMR][1000 genomes]
rs751819	0.88[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs8025600	0.88[ASW][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs8027324	0.96[YRI][hapmap]
rs8029983	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs8034420	0.93[AMR][1000 genomes]
rs8042179	1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs8042662	1.00[YRI][hapmap]

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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45881000-45908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:45881000-45908800	Weak transcription	Esophagus	oesophagus
3	chr15:45881200-45909000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:45882000-45908600	Weak transcription	NHLF	lung
5	chr15:45889800-45908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:45890200-45908800	Weak transcription	A549	lung
7	chr15:45896800-45912400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:45898400-45911000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:45898800-45909200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:45898800-45911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:45899400-45909000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45899600-45912400	Weak transcription	HSMMtube	muscle
13	chr15:45900800-45908800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:45900800-45908800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:45900800-45911800	Weak transcription	Primary B cells from cord blood	blood
16	chr15:45901000-45909000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:45901600-45908800	Weak transcription	HMEC	breast
18	chr15:45901600-45909400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:45901800-45908800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:45902200-45907200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:45902200-45910200	Weak transcription	Fetal Brain Female	brain
22	chr15:45905400-45908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:45905600-45908400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:45905600-45908600	Weak transcription	Hela-S3	cervix
25	chr15:45905600-45908600	Weak transcription	NHEK	skin
26	chr15:45905600-45909000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:45905600-45909000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:45905600-45909000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:45905600-45909000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:45905600-45909000	Weak transcription	NHDF-Ad	bronchial
31	chr15:45905800-45908800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:45906200-45909800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:45906600-45907000	Enhancers	Colon Smooth Muscle	Colon
34	chr15:45906800-45907000	Enhancers	Brain Anterior Caudate	brain
35	chr15:45906800-45907000	Enhancers	Brain Hippocampus Middle	brain

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