Variant report

Variant	rs17820461
Chromosome Location	chr15:57853584-57853585
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:57850033..57853675-chr15:57854841..57859589,5	K562	blood:
2	chr15:57851773..57853797-chr15:57903678..57905009,17	MCF-7	breast:
3	chr15:57852165..57854833-chr15:57859167..57860692,2	MCF-7	breast:
4	chr15:57852740..57853861-chr15:57903786..57904809,7	MCF-7	breast:
5	chr15:57852020..57854891-chr15:57910947..57913888,2	MCF-7	breast:
6	chr15:57852885..57853782-chr15:57947733..57948335,2	MCF-7	breast:
7	chr15:57853056..57853844-chr15:58513573..58514501,2	K562	blood:
8	chr15:57852958..57853665-chr15:57933273..57933872,2	MCF-7	breast:

No data

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11856	0.83[AMR][1000 genomes]
rs11856674	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12439291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439665	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12439793	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1626448	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1630903	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1666573	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1690316	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1690317	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1690318	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16977600	0.83[AFR][1000 genomes]
rs17820431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820449	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17820467	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908191	0.81[EUR][1000 genomes]
rs1908192	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2131730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131733	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2270487	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2270488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2279606	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2635389	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2922231	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2922232	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932208	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932209	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2934418	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774962	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55916627	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55952634	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56091272	0.81[AFR][1000 genomes]
rs56362917	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59368768	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66802357	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67336499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166305	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171354	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174359	0.83[AFR][1000 genomes]
rs72741522	0.94[ASN][1000 genomes]
rs72741528	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74018224	0.81[AFR][1000 genomes]
rs8025786	0.92[ASN][1000 genomes]
rs8038795	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs937248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh 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	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57844600-57859000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:57844800-57857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:57845200-57857600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:57846800-57861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57847000-57854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:57847200-57854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:57847600-57854400	Weak transcription	Pancreas	Pancrea
8	chr15:57847600-57859200	Weak transcription	Right Ventricle	heart
9	chr15:57847800-57853600	Weak transcription	Fetal Stomach	stomach
10	chr15:57847800-57859000	Weak transcription	Gastric	stomach
11	chr15:57847800-57859200	Weak transcription	Ovary	ovary
12	chr15:57847800-57859200	Weak transcription	Right Atrium	heart
13	chr15:57850200-57854400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:57851800-57853600	Enhancers	Liver	Liver
15	chr15:57852000-57856400	Enhancers	Stomach Mucosa	stomach
16	chr15:57852200-57853800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:57852200-57854000	Enhancers	A549	lung
18	chr15:57852400-57853600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:57852400-57853600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:57852400-57853800	Enhancers	Fetal Intestine Small	intestine
21	chr15:57852400-57854000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:57852400-57854000	Enhancers	Fetal Intestine Large	intestine
23	chr15:57852400-57855400	Enhancers	Stomach Smooth Muscle	stomach
24	chr15:57852400-57855600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:57852600-57853600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:57852800-57853600	Enhancers	Duodenum Mucosa	Duodenum
27	chr15:57853000-57853600	Enhancers	Adipose Nuclei	Adipose
28	chr15:57853000-57853600	Enhancers	Colon Smooth Muscle	Colon
29	chr15:57853000-57853800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr15:57853000-57854000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:57853200-57854000	Enhancers	Fetal Muscle Leg	muscle
32	chr15:57853200-57854000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr15:57853200-57854200	Enhancers	HMEC	breast
34	chr15:57853200-57854400	Enhancers	Primary B cells from cord blood	blood
35	chr15:57853200-57854600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:57853200-57855000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:57853200-57856200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr15:57853200-57856400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr15:57853400-57853600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr15:57853400-57853600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:57853400-57853600	Enhancers	GM12878-XiMat	blood
42	chr15:57853400-57853800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr15:57853400-57853800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr15:57853400-57853800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr15:57853400-57853800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:57853400-57853800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:57853400-57853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:57853400-57853800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:57853400-57853800	Flanking Active TSS	Fetal Heart	heart
50	chr15:57853400-57853800	Enhancers	Rectal Smooth Muscle	rectum

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