Variant report

Variant	rs12253887
Chromosome Location	chr10:52220401-52220402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52220084..52221898-chr10:52222216..52224809,2	MCF-7	breast:
2	chr10:52220256..52222219-chr10:52225447..52227961,2	MCF-7	breast:
3	chr10:52218961..52222149-chr10:52229280..52232143,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10159614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10825837	1.00[AMR][1000 genomes]
rs11005454	0.81[AFR][1000 genomes]
rs11005901	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11005920	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11006017	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11815109	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12244472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12245522	1.00[ASN][1000 genomes]
rs12246357	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12251096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12253726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12255967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262002	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12265260	0.82[ASN][1000 genomes]
rs12265364	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61152656	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73316672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73316673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73316690	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73332908	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73332909	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7358033	1.00[ASN][1000 genomes]
rs7916018	1.00[AMR][1000 genomes];0.94[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
2	chr10:52192400-52230400	Weak transcription	HSMM	muscle
3	chr10:52197800-52229800	Weak transcription	Gastric	stomach
4	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
5	chr10:52207800-52221800	Weak transcription	Psoas Muscle	Psoas
6	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
7	chr10:52208200-52229600	Weak transcription	Right Ventricle	heart
8	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:52209600-52229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:52211600-52223800	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:52211800-52229400	Weak transcription	NHEK	skin
12	chr10:52212800-52229400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:52212800-52229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:52215200-52228800	Weak transcription	HepG2	liver
16	chr10:52215200-52229000	Weak transcription	Brain Angular Gyrus	brain
17	chr10:52215600-52228600	Weak transcription	HSMMtube	muscle
18	chr10:52215800-52228600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:52216000-52221600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr10:52216400-52228600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:52217200-52229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:52218000-52221200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:52218200-52228800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:52218200-52230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr10:52218400-52229400	Weak transcription	A549	lung
27	chr10:52218600-52228400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:52219000-52221200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:52219000-52221400	Weak transcription	Fetal Brain Female	brain
30	chr10:52219000-52221400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr10:52219000-52223400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr10:52219000-52223600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr10:52219400-52220600	Strong transcription	Primary T cells from cord blood	blood
34	chr10:52219400-52220600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:52219400-52220600	Strong transcription	Liver	Liver
36	chr10:52219400-52220600	Strong transcription	Fetal Muscle Leg	muscle
37	chr10:52219400-52220600	Strong transcription	Left Ventricle	heart
38	chr10:52219400-52220600	Strong transcription	GM12878-XiMat	blood
39	chr10:52219400-52220800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr10:52219400-52226000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr10:52219600-52220600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:52219600-52220600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr10:52219600-52220600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr10:52219600-52220600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr10:52219600-52220600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:52219600-52220600	Strong transcription	Adipose Nuclei	Adipose
47	chr10:52219600-52220600	Strong transcription	Thymus	Thymus
48	chr10:52219600-52220600	Strong transcription	K562	blood
49	chr10:52219600-52220800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:52219800-52220600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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