Variant report

Variant	rs28418905
Chromosome Location	chr2:209187842-209187843
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10173938	0.84[EUR][1000 genomes]
rs10174541	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10176626	0.86[EUR][1000 genomes]
rs10177810	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186350	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10189031	0.84[EUR][1000 genomes]
rs10190458	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10194539	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10198535	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10497897	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10497898	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10932260	0.86[EUR][1000 genomes]
rs11538998	1.00[ASN][1000 genomes]
rs11885913	1.00[ASN][1000 genomes]
rs11891163	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11898653	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11901959	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12185709	0.84[EUR][1000 genomes]
rs12475932	0.83[EUR][1000 genomes]
rs12694104	0.84[EUR][1000 genomes]
rs12991283	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12998277	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13395035	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13395304	0.82[EUR][1000 genomes]
rs13400356	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13407268	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13407897	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13412043	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1584200	0.86[EUR][1000 genomes]
rs17699838	1.00[ASN][1000 genomes]
rs17700235	1.00[ASN][1000 genomes]
rs1866046	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1900239	0.86[EUR][1000 genomes]
rs2304545	0.90[EUR][1000 genomes]
rs2363465	0.84[EUR][1000 genomes]
rs2363466	0.84[EUR][1000 genomes]
rs28885800	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35217101	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35293936	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4673391	0.86[EUR][1000 genomes]
rs4673393	0.83[EUR][1000 genomes]
rs4675748	0.86[EUR][1000 genomes]
rs4675751	0.86[EUR][1000 genomes]
rs66826643	1.00[ASN][1000 genomes]
rs66887797	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6724208	0.86[EUR][1000 genomes]
rs6725527	1.00[ASN][1000 genomes]
rs6736599	0.86[EUR][1000 genomes]
rs67660353	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67669827	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67965883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056463	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7355562	0.95[EUR][1000 genomes]
rs7557303	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7587752	0.86[EUR][1000 genomes]
rs7592472	0.90[EUR][1000 genomes]
rs9288392	0.86[EUR][1000 genomes]
rs999890	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999891	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
2	chr2:209160000-209188800	Weak transcription	Small Intestine	intestine
3	chr2:209165800-209204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:209166200-209189600	Weak transcription	Pancreas	Pancrea
5	chr2:209166600-209189000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:209170000-209190000	Weak transcription	Right Ventricle	heart
7	chr2:209170200-209189600	Weak transcription	Colonic Mucosa	Colon
8	chr2:209179000-209190600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:209179000-209220600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:209180400-209189800	Weak transcription	Esophagus	oesophagus
11	chr2:209180400-209189800	Weak transcription	Hela-S3	cervix
12	chr2:209180400-209190000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:209180600-209189000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:209180600-209190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:209180600-209190000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:209180600-209190200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:209180600-209224600	Strong transcription	Fetal Thymus	thymus
18	chr2:209182400-209224200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:209182600-209188800	Weak transcription	HMEC	breast
20	chr2:209183000-209189000	Weak transcription	Brain Angular Gyrus	brain
21	chr2:209183200-209188800	Weak transcription	Fetal Kidney	kidney
22	chr2:209183200-209188800	Weak transcription	Gastric	stomach
23	chr2:209183200-209189600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:209183200-209189800	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:209183200-209190000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:209183200-209190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:209183200-209193800	Weak transcription	Fetal Brain Male	brain
28	chr2:209183400-209188800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:209183400-209188800	Weak transcription	NHLF	lung
30	chr2:209183400-209189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:209183400-209189000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:209183400-209189200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:209183400-209189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:209183400-209189600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:209183600-209188800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:209183600-209189000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:209183800-209190000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:209183800-209190200	Weak transcription	NHEK	skin
39	chr2:209184000-209188800	Weak transcription	Brain Germinal Matrix	brain
40	chr2:209184000-209189200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:209184400-209188800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:209184400-209188800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:209184400-209188800	Weak transcription	HUVEC	blood vessel
44	chr2:209184400-209188800	Weak transcription	NH-A	brain
45	chr2:209184400-209189400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:209184400-209189800	Weak transcription	Psoas Muscle	Psoas
47	chr2:209184400-209190000	Weak transcription	Spleen	Spleen
48	chr2:209184600-209188800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:209184600-209189200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:209184600-209201400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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