Variant report

Variant	rs72946417
Chromosome Location	chr2:98380394-98380395
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	chr2:98378430..98380817-chr2:98383033..98385975,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11892146	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11898394	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11903844	0.82[AFR][1000 genomes]
rs1503201	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	1.00[AMR][1000 genomes]
rs17022209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022736	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17025339	1.00[AMR][1000 genomes]
rs2309318	0.90[AFR][1000 genomes]
rs35774346	0.86[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60828800	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61712471	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6543226	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6736475	1.00[AMR][1000 genomes]
rs6737992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	0.82[AFR][1000 genomes]
rs6746457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942830	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942834	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942836	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942856	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942871	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942882	0.86[AFR][1000 genomes]
rs72942885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944825	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946410	0.90[AFR][1000 genomes]
rs72946421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579764	0.92[AFR][1000 genomes];1.00[AMR][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	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:98359200-98382400	Weak transcription	Psoas Muscle	Psoas
3	chr2:98366200-98400000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:98366400-98384600	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr2:98367200-98385000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:98368000-98393800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:98368400-98383600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:98369200-98381200	Weak transcription	Fetal Heart	heart
10	chr2:98369600-98398800	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:98369800-98384800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:98370200-98392600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:98370400-98382800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:98370400-98383600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:98370400-98386400	Strong transcription	Fetal Intestine Small	intestine
16	chr2:98370600-98381800	Strong transcription	Lung	lung
17	chr2:98370600-98384400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr2:98370600-98384400	Strong transcription	Placenta	Placenta
19	chr2:98370600-98392400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:98370600-98393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:98370600-98407600	Weak transcription	HUVEC	blood vessel
22	chr2:98370800-98384200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:98370800-98384400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:98370800-98384400	Strong transcription	Fetal Stomach	stomach
25	chr2:98371000-98383000	Strong transcription	Brain Angular Gyrus	brain
26	chr2:98371000-98383000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:98371000-98383400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr2:98371000-98384800	Strong transcription	Fetal Intestine Large	intestine
29	chr2:98371200-98383000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:98371200-98383000	Strong transcription	Brain Anterior Caudate	brain
31	chr2:98371200-98383000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr2:98371200-98383200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:98371200-98383400	Strong transcription	Colonic Mucosa	Colon
34	chr2:98371200-98384400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:98371200-98384400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:98371200-98387400	Strong transcription	Liver	Liver
37	chr2:98371200-98398600	Strong transcription	Primary B cells from cord blood	blood
38	chr2:98371400-98383400	Strong transcription	Brain Hippocampus Middle	brain
39	chr2:98371400-98383400	Strong transcription	Fetal Brain Female	brain
40	chr2:98371400-98383400	Strong transcription	Dnd41	blood
41	chr2:98371800-98384200	Strong transcription	Thymus	Thymus
42	chr2:98371800-98384400	Strong transcription	NHLF	lung
43	chr2:98372200-98384600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:98372400-98380400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:98372400-98384400	Strong transcription	HepG2	liver
46	chr2:98372600-98383800	Weak transcription	Right Atrium	heart
47	chr2:98373200-98382600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:98373200-98384400	Strong transcription	Ovary	ovary
49	chr2:98373200-98384400	Strong transcription	Pancreas	Pancrea
50	chr2:98373400-98383400	Strong transcription	Rectal Smooth Muscle	rectum

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