Variant report

Variant	rs226401
Chromosome Location	chr12:9250459-9250460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9248855..9251571-chr12:9264323..9266629,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743598	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771308	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10842839	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10842849	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11048839	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs113973	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805682	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2193006	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2216143	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226380	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226381	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226382	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226386	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226387	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226388	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226389	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226390	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226391	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226392	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226394	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226403	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226408	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226415	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3759277	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4882977	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6487584	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71453666	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7295733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7964085	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7965790	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7976808	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
2	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
3	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:9236600-9258800	Weak transcription	Fetal Heart	heart
7	chr12:9237200-9252200	Weak transcription	Psoas Muscle	Psoas
8	chr12:9237200-9261200	Strong transcription	Liver	Liver
9	chr12:9237200-9265200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:9237400-9264200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:9237800-9258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:9238600-9265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:9239400-9262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:9239400-9264000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:9239600-9265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:9240800-9267600	Weak transcription	Fetal Intestine Large	intestine
17	chr12:9241200-9262800	Strong transcription	Adipose Nuclei	Adipose
18	chr12:9241600-9264000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:9243000-9251400	Weak transcription	Primary T cells from cord blood	blood
20	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
21	chr12:9243400-9265400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:9243800-9252000	Strong transcription	HepG2	liver
23	chr12:9244200-9265200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:9245000-9251200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:9245000-9266000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:9245200-9251800	Weak transcription	Colonic Mucosa	Colon
27	chr12:9245200-9254000	Weak transcription	Gastric	stomach
28	chr12:9245200-9259200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:9245400-9256600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:9245600-9254600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:9246200-9251200	Weak transcription	Pancreas	Pancrea
32	chr12:9246200-9265200	Weak transcription	Fetal Brain Male	brain
33	chr12:9246600-9266000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:9246600-9268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:9246800-9250600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:9246800-9251200	Weak transcription	Aorta	Aorta
37	chr12:9246800-9251200	Weak transcription	Right Ventricle	heart
38	chr12:9246800-9251200	Weak transcription	Spleen	Spleen
39	chr12:9246800-9252400	Weak transcription	Brain Substantia Nigra	brain
40	chr12:9246800-9253400	Weak transcription	Lung	lung
41	chr12:9248000-9257200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:9248000-9262600	Strong transcription	Left Ventricle	heart
43	chr12:9248800-9250600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:9249000-9251600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:9249200-9250600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:9249200-9251400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:9249200-9253400	Weak transcription	Ovary	ovary
48	chr12:9249400-9268800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:9249600-9251200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:9249600-9251200	Weak transcription	Rectal Mucosa Donor 31	rectum

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