Variant report

Variant	rs13407897
Chromosome Location	chr2:209173592-209173593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10173938	0.95[EUR][1000 genomes]
rs10174541	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10176626	0.98[EUR][1000 genomes]
rs10177810	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10186350	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10189031	0.95[EUR][1000 genomes]
rs10190458	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10194539	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10198535	0.98[EUR][1000 genomes]
rs10497897	1.00[EUR][1000 genomes]
rs10497898	1.00[EUR][1000 genomes]
rs10932260	0.98[EUR][1000 genomes]
rs11898653	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11901959	1.00[EUR][1000 genomes]
rs12185709	0.95[EUR][1000 genomes]
rs12475932	0.94[EUR][1000 genomes]
rs12694104	0.95[EUR][1000 genomes]
rs13392540	0.86[EUR][1000 genomes]
rs13395304	0.93[EUR][1000 genomes]
rs13407268	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13412043	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1584200	0.98[EUR][1000 genomes]
rs1900239	0.98[EUR][1000 genomes]
rs2304545	0.84[EUR][1000 genomes]
rs2363465	0.95[EUR][1000 genomes]
rs2363466	0.95[EUR][1000 genomes]
rs28418905	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4673391	0.98[EUR][1000 genomes]
rs4673393	0.95[EUR][1000 genomes]
rs4675748	0.98[EUR][1000 genomes]
rs4675751	0.98[EUR][1000 genomes]
rs66887797	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6724208	0.98[EUR][1000 genomes]
rs6736599	0.98[EUR][1000 genomes]
rs67669827	1.00[EUR][1000 genomes]
rs67965883	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73056463	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7355562	0.88[EUR][1000 genomes]
rs7557303	1.00[EUR][1000 genomes]
rs7587752	0.98[EUR][1000 genomes]
rs7592472	0.84[EUR][1000 genomes]
rs9288392	0.98[EUR][1000 genomes]
rs999890	0.90[EUR][1000 genomes]
rs999891	0.90[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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 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	chr2:209139400-209180000	Strong transcription	Fetal Thymus	thymus
2	chr2:209141200-209180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
4	chr2:209149600-209179800	Strong transcription	Dnd41	blood
5	chr2:209156000-209180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:209157200-209173600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:209159200-209182200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:209159800-209179400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:209160000-209188800	Weak transcription	Small Intestine	intestine
10	chr2:209162400-209174600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:209163000-209187400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:209163200-209177000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr2:209163200-209180600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:209163200-209187400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:209163400-209174600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:209163400-209180600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:209163400-209187400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:209163600-209180600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:209163600-209182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:209164800-209179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:209165800-209180000	Weak transcription	Aorta	Aorta
22	chr2:209165800-209204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:209166200-209189600	Weak transcription	Pancreas	Pancrea
24	chr2:209166600-209189000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:209167000-209179600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:209167200-209176600	Weak transcription	Fetal Heart	heart
27	chr2:209167200-209177400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:209167200-209179600	Weak transcription	NHEK	skin
29	chr2:209169800-209180000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:209170000-209176400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:209170000-209178400	Weak transcription	Fetal Stomach	stomach
32	chr2:209170000-209179000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:209170000-209179000	Weak transcription	Lung	lung
34	chr2:209170000-209179000	Weak transcription	Thymus	Thymus
35	chr2:209170000-209179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:209170000-209179200	Weak transcription	A549	lung
37	chr2:209170000-209179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:209170000-209179400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:209170000-209179400	Weak transcription	Gastric	stomach
40	chr2:209170000-209179600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:209170000-209179600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:209170000-209179800	Weak transcription	Fetal Brain Male	brain
43	chr2:209170000-209179800	Weak transcription	Ovary	ovary
44	chr2:209170000-209179800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:209170000-209179800	Weak transcription	Hela-S3	cervix
46	chr2:209170000-209180000	Weak transcription	Esophagus	oesophagus
47	chr2:209170000-209182200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:209170000-209182200	Weak transcription	Spleen	Spleen
49	chr2:209170000-209183000	Weak transcription	Psoas Muscle	Psoas
50	chr2:209170000-209190000	Weak transcription	Right Ventricle	heart

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