Variant report

Variant	rs11168909
Chromosome Location	chr12:49576875-49576876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49521045..49522741-chr12:49576322..49578574,2	K562	blood:
2	chr12:49455381..49457675-chr12:49576315..49579055,2	MCF-7	breast:
3	chr12:49523810..49525846-chr12:49575368..49579813,5	K562	blood:
4	chr12:49555555..49558030-chr12:49574944..49577744,2	MCF-7	breast:
5	chr12:49524206..49526394-chr12:49575960..49578007,2	MCF-7	breast:
6	chr12:49523732..49525684-chr12:49574789..49577975,3	K562	blood:

Variant related genes	Relation type
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1039225	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1056875	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783307	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783308	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10875922	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875924	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875925	0.87[EUR][1000 genomes]
rs10875927	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875928	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875929	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875930	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875931	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168867	0.81[EUR][1000 genomes]
rs11168874	0.84[EUR][1000 genomes]
rs11168882	0.88[EUR][1000 genomes]
rs11168884	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168885	0.90[EUR][1000 genomes]
rs11168888	0.85[EUR][1000 genomes]
rs11168890	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168894	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168895	0.84[EUR][1000 genomes]
rs11168901	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168902	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168903	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168904	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168910	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12227296	0.85[EUR][1000 genomes]
rs12227610	0.89[EUR][1000 genomes]
rs12227770	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229524	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12229529	0.82[EUR][1000 genomes]
rs12306494	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12318740	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12579015	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1476137	0.84[EUR][1000 genomes]
rs1476138	0.83[EUR][1000 genomes]
rs1874908	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991427	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1991428	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2016107	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114845	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2114846	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2162643	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2162644	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2241727	0.83[EUR][1000 genomes]
rs2334930	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2334931	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2753	0.83[EUR][1000 genomes]
rs2878287	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35884657	0.82[EUR][1000 genomes]
rs57853986	0.83[EUR][1000 genomes]
rs58336603	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58711211	0.85[EUR][1000 genomes]
rs6580701	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580703	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697624	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73110168	0.84[EUR][1000 genomes]
rs7311346	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731350	0.84[EUR][1000 genomes]
rs7953169	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954521	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7954530	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957998	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976890	0.82[EUR][1000 genomes]
rs9325145	0.86[EUR][1000 genomes]
rs9739878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9788139	0.80[EUR][1000 genomes]
rs9788140	0.80[EUR][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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	esv3417605	chr12:49521878-49578961	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
5	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49570200-49577600	Weak transcription	Primary T cells from cord blood	blood
2	chr12:49570400-49577400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:49570400-49577400	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:49570400-49577600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:49570600-49581000	Weak transcription	GM12878-XiMat	blood
6	chr12:49570800-49578400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:49571800-49577600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:49574000-49577200	Weak transcription	Fetal Brain Female	brain
9	chr12:49574200-49578600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:49574200-49580600	Weak transcription	Primary B cells from cord blood	blood
11	chr12:49574800-49577000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:49575000-49578400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:49575200-49577400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:49575200-49578200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:49575200-49578800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:49575600-49577200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:49575600-49577400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:49575600-49577400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:49575600-49577600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:49575600-49577600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:49575600-49577800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:49575600-49577800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:49575800-49577400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:49575800-49577400	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:49575800-49577800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:49575800-49578000	Weak transcription	Fetal Stomach	stomach
27	chr12:49575800-49578200	Weak transcription	Fetal Lung	lung
28	chr12:49576000-49577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:49576000-49577600	Weak transcription	Adipose Nuclei	Adipose
30	chr12:49576000-49577600	Weak transcription	HSMM	muscle
31	chr12:49576000-49577600	Weak transcription	NH-A	brain
32	chr12:49576000-49577600	Weak transcription	NHDF-Ad	bronchial
33	chr12:49576000-49577800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:49576000-49577800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:49576000-49577800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:49576000-49577800	Weak transcription	Left Ventricle	heart
37	chr12:49576000-49577800	Weak transcription	Thymus	Thymus
38	chr12:49576000-49578200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:49576000-49578200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:49576000-49578200	Weak transcription	Fetal Intestine Large	intestine
41	chr12:49576000-49578600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:49576000-49580800	Weak transcription	A549	lung
43	chr12:49576200-49577200	Weak transcription	Brain Anterior Caudate	brain
44	chr12:49576200-49577800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:49576200-49577800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:49576200-49577800	Weak transcription	Osteobl	bone
47	chr12:49576200-49578000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:49576200-49578200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:49576200-49578600	Weak transcription	Placenta	Placenta
50	chr12:49576200-49579200	Weak transcription	Fetal Intestine Small	intestine

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