Variant report

Variant	rs12486470
Chromosome Location	chr3:50094271-50094272
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11130223	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130225	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130230	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130237	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130239	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130240	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11916261	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11916999	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920034	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923132	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11924670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925156	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11928995	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486808	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12486832	0.92[EUR][1000 genomes]
rs12489386	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12490944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12492291	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493565	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12494077	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494172	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494916	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495114	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495831	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12629129	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12629553	0.85[EUR][1000 genomes]
rs12629677	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12630917	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12630959	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631248	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631306	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631309	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631608	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12632751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636045	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636232	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636669	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12637222	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12637457	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12637681	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12638046	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13100903	0.94[ASN][1000 genomes]
rs1317215	0.88[EUR][1000 genomes]
rs13326300	0.88[EUR][1000 genomes]
rs2003485	0.87[ASN][1000 genomes]
rs2023951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023952	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478136	0.88[EUR][1000 genomes]
rs35333166	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41291716	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55643042	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57009357	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57575459	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58025924	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58621288	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58766761	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59802870	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61491513	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61729114	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62260756	0.88[EUR][1000 genomes]
rs62260770	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260771	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262060	0.88[EUR][1000 genomes]
rs62262095	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262096	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262099	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262100	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262104	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62262105	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262116	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262136	0.81[AMR][1000 genomes]
rs62262138	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262144	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262145	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62262148	0.92[EUR][1000 genomes]
rs62263578	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62263580	1.00[EUR][1000 genomes]
rs62263584	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263586	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263588	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263591	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263596	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263597	0.88[ASN][1000 genomes]
rs62263600	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797500	0.88[EUR][1000 genomes]
rs9813644	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859813	0.88[EUR][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	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 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	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
3	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:50072800-50095200	Weak transcription	Fetal Heart	heart
5	chr3:50078400-50102400	Weak transcription	Psoas Muscle	Psoas
6	chr3:50079200-50095200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:50079200-50095200	Weak transcription	K562	blood
8	chr3:50082000-50113600	Strong transcription	Primary T cells from cord blood	blood
9	chr3:50082000-50115600	Strong transcription	Fetal Intestine Large	intestine
10	chr3:50082200-50112000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:50082200-50116000	Strong transcription	Fetal Muscle Leg	muscle
12	chr3:50082400-50113400	Strong transcription	Primary B cells from cord blood	blood
13	chr3:50082400-50115800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:50082400-50116200	Strong transcription	Fetal Thymus	thymus
15	chr3:50082600-50116200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:50083400-50113200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:50083800-50098000	Strong transcription	Fetal Intestine Small	intestine
18	chr3:50083800-50111600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:50084000-50105200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:50084000-50113400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:50084000-50114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:50084000-50114800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:50084200-50095000	Weak transcription	Aorta	Aorta
24	chr3:50084200-50115000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:50084200-50116600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:50084400-50112200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:50084400-50115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:50084600-50104600	Strong transcription	Placenta	Placenta
29	chr3:50084600-50113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:50084600-50114600	Strong transcription	Adipose Nuclei	Adipose
31	chr3:50084800-50113400	Strong transcription	Dnd41	blood
32	chr3:50085000-50113600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:50085000-50114800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:50085000-50115800	Strong transcription	Liver	Liver
35	chr3:50085200-50109200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr3:50085200-50111600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:50085200-50115800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:50085400-50113800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:50085600-50113200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:50086000-50095000	Weak transcription	Brain Angular Gyrus	brain
41	chr3:50086000-50095200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:50086000-50095200	Weak transcription	Esophagus	oesophagus
43	chr3:50086200-50095200	Weak transcription	Right Ventricle	heart
44	chr3:50086400-50095000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:50086400-50095200	Weak transcription	Fetal Brain Male	brain
46	chr3:50086600-50104800	Weak transcription	Stomach Mucosa	stomach
47	chr3:50086800-50095200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:50087200-50115800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:50087800-50115800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:50088000-50095400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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