Variant report

Variant	rs57575459
Chromosome Location	chr3:50053514-50053515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11130223	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130225	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130230	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130237	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130239	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130240	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916261	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916999	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11920034	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11923132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11924711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11925156	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486470	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12486808	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486832	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489386	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490944	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492291	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12493565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494077	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494172	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494916	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495114	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12495831	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629129	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629553	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629677	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630917	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630959	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631248	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12631306	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631309	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12636045	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12636669	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637222	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637457	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637681	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638046	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317215	0.96[EUR][1000 genomes]
rs13326300	0.96[EUR][1000 genomes]
rs2023951	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2023952	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28478136	0.96[EUR][1000 genomes]
rs35333166	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41291716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55643042	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57009357	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58025924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58621288	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59802870	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61263937	0.85[EUR][1000 genomes]
rs61491513	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729114	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260717	0.84[EUR][1000 genomes]
rs62260756	0.96[EUR][1000 genomes]
rs62262060	0.96[EUR][1000 genomes]
rs62262095	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262096	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262099	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262100	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262104	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262105	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262116	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262117	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262136	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262144	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262148	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263578	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263580	0.92[EUR][1000 genomes]
rs62263584	0.92[EUR][1000 genomes]
rs62263586	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263588	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263590	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263591	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263600	0.87[AMR][1000 genomes]
rs6797500	0.96[EUR][1000 genomes]
rs9813644	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9859813	0.96[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	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	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
5	chr3:50010800-50087000	Weak transcription	NHLF	lung
6	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
8	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:50028000-50056400	Weak transcription	Ovary	ovary
10	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
11	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
12	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
13	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
14	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
15	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
17	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
18	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:50038800-50056800	Weak transcription	HepG2	liver
21	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:50040400-50056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:50041400-50057000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:50041600-50055200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:50041600-50056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:50041600-50057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:50041600-50058200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:50041600-50061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
32	chr3:50041600-50065200	Weak transcription	NH-A	brain
33	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
34	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
35	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
37	chr3:50042400-50054600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:50044000-50057400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:50046200-50059000	Strong transcription	Dnd41	blood
42	chr3:50046600-50055600	Weak transcription	HSMMtube	muscle
43	chr3:50046800-50053600	Weak transcription	Adipose Nuclei	Adipose
44	chr3:50046800-50056200	Weak transcription	NHEK	skin
45	chr3:50046800-50056600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:50046800-50056600	Weak transcription	Osteobl	bone
47	chr3:50046800-50064600	Weak transcription	Aorta	Aorta
48	chr3:50046800-50065400	Weak transcription	Fetal Kidney	kidney
49	chr3:50046800-50085800	Weak transcription	HMEC	breast
50	chr3:50047000-50061400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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