Variant report

Variant	rs12240040
Chromosome Location	chr1:172150032-172150033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172146908..172150355-chr1:172151675..172155662,5	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10489296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10911275	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911278	1.00[EUR][1000 genomes]
rs11800007	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11800549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11800998	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804505	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807738	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810189	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277134	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17277295	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17362060	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4644529	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6690462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787394	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172146600-172150200	Enhancers	Stomach Mucosa	stomach
2	chr1:172146800-172152000	Enhancers	Fetal Intestine Small	intestine
3	chr1:172147400-172154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:172147600-172151200	Enhancers	Fetal Intestine Large	intestine
5	chr1:172148800-172152000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:172149000-172150400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:172149000-172152800	Enhancers	Fetal Stomach	stomach
8	chr1:172149200-172150200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:172149200-172150600	Enhancers	Brain Hippocampus Middle	brain
10	chr1:172149400-172150200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:172149400-172150200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:172149400-172150200	Weak transcription	Ovary	ovary
13	chr1:172149400-172150400	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:172149400-172150600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:172149400-172151000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:172149400-172151000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr1:172149400-172151600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:172149400-172152000	Enhancers	Fetal Heart	heart
19	chr1:172149600-172150200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr1:172149600-172150800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr1:172149600-172151400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:172149600-172153600	Weak transcription	Small Intestine	intestine
23	chr1:172149800-172150200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:172149800-172150200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:172149800-172150200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:172149800-172150200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:172149800-172150200	Enhancers	Colonic Mucosa	Colon
28	chr1:172149800-172150200	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr1:172149800-172150200	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:172149800-172150200	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:172149800-172150200	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr1:172149800-172150200	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr1:172149800-172150200	Enhancers	Hela-S3	cervix
34	chr1:172149800-172150200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr1:172149800-172150400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr1:172149800-172150400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:172149800-172150600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:172149800-172150600	Flanking Active TSS	Fetal Kidney	kidney
39	chr1:172149800-172151000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:172149800-172151000	Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:172149800-172151000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:172149800-172151000	Active TSS	Aorta	Aorta
43	chr1:172149800-172151000	Flanking Active TSS	Osteobl	bone
44	chr1:172149800-172151200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:172149800-172151200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:172149800-172151400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:172149800-172151600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:172149800-172151800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:172149800-172152000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:172150000-172150200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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