Variant report

Variant	rs12569909
Chromosome Location	chr10:52206068-52206069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52199893..52201805-chr10:52203419..52206353,2	K562	blood:
2	chr10:52199832..52201783-chr10:52205010..52207996,2	K562	blood:
3	chr10:52205018..52207275-chr10:52208776..52210388,2	K562	blood:
4	chr10:52201084..52203471-chr10:52204714..52206588,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082515	0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs10218880	1.00[CEU][hapmap]
rs10218927	1.00[CEU][hapmap]
rs1028534	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10826014	0.91[JPT][hapmap]
rs11005720	0.87[JPT][hapmap]
rs11006224	1.00[CEU][hapmap]
rs1203380	0.91[JPT][hapmap]
rs1212555	0.91[JPT][hapmap]
rs12243444	1.00[CEU][hapmap]
rs12261465	1.00[CEU][hapmap]
rs12262564	1.00[CEU][hapmap]
rs12569801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12573520	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937491	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937722	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16937771	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16937775	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16937786	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16937874	1.00[CEU][hapmap]
rs17179881	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1880071	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064760	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2983346	0.88[ASN][1000 genomes]
rs2983349	0.91[ASN][1000 genomes]
rs3739990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41427847	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57015168	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57748270	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57999700	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58383805	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58642196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59510112	0.85[ASN][1000 genomes]
rs59512026	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66546375	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67761241	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73332935	0.82[AMR][1000 genomes]
rs910818	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
7	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
9	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
12	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
13	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:52192400-52219400	Weak transcription	Liver	Liver
15	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
19	chr10:52192400-52230400	Weak transcription	HSMM	muscle
20	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:52193400-52206200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:52197600-52207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:52197800-52229800	Weak transcription	Gastric	stomach
25	chr10:52198200-52207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:52198400-52207400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:52199200-52207400	Weak transcription	Brain Anterior Caudate	brain
28	chr10:52200200-52207600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr10:52200800-52216000	Weak transcription	K562	blood
30	chr10:52201000-52214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:52201400-52206200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr10:52202200-52214000	Weak transcription	Fetal Heart	heart
33	chr10:52203000-52206200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr10:52203000-52219400	Weak transcription	Ovary	ovary
35	chr10:52203200-52219400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:52203800-52219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
38	chr10:52204600-52206200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:52205400-52206600	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr10:52205600-52206600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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