Variant report

Variant	rs12479594
Chromosome Location	chr20:13513619-13513620
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1024208	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028849	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12329620	1.00[CEU][hapmap]
rs12479480	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12479483	1.00[EUR][1000 genomes]
rs12479520	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12479746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479849	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12480005	1.00[EUR][1000 genomes]
rs12480101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12480131	1.00[ASN][1000 genomes]
rs12480217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12480263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12480266	1.00[JPT][hapmap]
rs12480276	1.00[JPT][hapmap]
rs12480277	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480285	1.00[EUR][1000 genomes]
rs12480426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480457	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12480493	1.00[EUR][1000 genomes]
rs12480587	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12480970	1.00[EUR][1000 genomes]
rs12480977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12481107	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481227	1.00[EUR][1000 genomes]
rs12481291	1.00[EUR][1000 genomes]
rs12481494	1.00[EUR][1000 genomes]
rs1321297	1.00[EUR][1000 genomes]
rs1535410	1.00[EUR][1000 genomes]
rs1812562	1.00[JPT][hapmap]
rs2145140	1.00[JPT][hapmap]
rs2180570	1.00[ASN][1000 genomes]
rs2327755	1.00[JPT][hapmap]
rs34573439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34988299	1.00[EUR][1000 genomes]
rs4471952	1.00[EUR][1000 genomes]
rs4502495	1.00[EUR][1000 genomes]
rs57602234	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033694	1.00[JPT][hapmap]
rs6033695	1.00[JPT][hapmap]
rs6033699	1.00[JPT][hapmap]
rs6033702	1.00[JPT][hapmap]
rs6033712	1.00[JPT][hapmap]
rs6033718	1.00[JPT][hapmap]
rs6033782	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6033802	1.00[ASN][1000 genomes]
rs60385063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60404222	1.00[AMR][1000 genomes]
rs6042069	1.00[JPT][hapmap]
rs6042077	1.00[JPT][hapmap]
rs6042081	1.00[JPT][hapmap]
rs6042083	1.00[JPT][hapmap]
rs6042084	1.00[JPT][hapmap]
rs6042089	1.00[JPT][hapmap]
rs6042093	1.00[JPT][hapmap]
rs6042108	1.00[JPT][hapmap]
rs6042111	1.00[JPT][hapmap]
rs6042113	1.00[JPT][hapmap]
rs6042130	1.00[JPT][hapmap]
rs6042136	1.00[JPT][hapmap]
rs6042142	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6042143	1.00[ASN][1000 genomes]
rs6042152	1.00[ASN][1000 genomes]
rs6042154	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6042212	1.00[JPT][hapmap]
rs6042234	1.00[ASN][1000 genomes]
rs6042241	1.00[ASN][1000 genomes]
rs6042242	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6042248	1.00[ASN][1000 genomes]
rs6042249	1.00[ASN][1000 genomes]
rs6042274	1.00[ASN][1000 genomes]
rs6042275	1.00[ASN][1000 genomes]
rs6042284	1.00[ASN][1000 genomes]
rs60686384	1.00[ASN][1000 genomes]
rs6079117	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105082	1.00[JPT][hapmap]
rs6105083	1.00[JPT][hapmap]
rs6105088	1.00[JPT][hapmap]
rs6105089	1.00[JPT][hapmap]
rs6105092	1.00[JPT][hapmap]
rs6105093	1.00[JPT][hapmap]
rs6105094	1.00[JPT][hapmap]
rs6105108	1.00[JPT][hapmap]
rs6105109	1.00[JPT][hapmap]
rs6105111	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105146	1.00[ASN][1000 genomes]
rs6109863	1.00[JPT][hapmap]
rs6109866	1.00[JPT][hapmap]
rs6109869	1.00[JPT][hapmap]
rs6109870	1.00[JPT][hapmap]
rs6109871	1.00[JPT][hapmap]
rs6109872	1.00[JPT][hapmap]
rs6109873	1.00[JPT][hapmap]
rs6109883	1.00[JPT][hapmap]
rs6109886	1.00[JPT][hapmap]
rs6109888	1.00[JPT][hapmap]
rs6109889	1.00[JPT][hapmap]
rs6109895	1.00[JPT][hapmap]
rs6109896	1.00[JPT][hapmap]
rs6109901	1.00[JPT][hapmap]
rs6109904	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6109972	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6109985	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs61152009	1.00[AFR][1000 genomes]
rs61343988	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61518689	1.00[ASN][1000 genomes]
rs7274078	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73254604	1.00[ASN][1000 genomes]
rs73264980	1.00[EUR][1000 genomes]
rs73270770	1.00[ASN][1000 genomes]
rs73899330	1.00[ASN][1000 genomes]
rs927122	1.00[JPT][hapmap]
rs9653627	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv912687	chr20:13507057-13591596	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
2	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
3	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr20:13494200-13516000	Weak transcription	Colonic Mucosa	Colon
8	chr20:13494400-13514800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr20:13494600-13516400	Weak transcription	Esophagus	oesophagus
10	chr20:13495800-13515000	Weak transcription	Fetal Brain Male	brain
11	chr20:13496000-13520200	Weak transcription	HSMMtube	muscle
12	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
13	chr20:13499200-13514600	Weak transcription	Brain Angular Gyrus	brain
14	chr20:13501200-13514600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:13502400-13516400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr20:13502800-13519200	Weak transcription	Lung	lung
17	chr20:13503000-13537600	Weak transcription	Psoas Muscle	Psoas
18	chr20:13503000-13538200	Weak transcription	Ovary	ovary
19	chr20:13504200-13527000	Strong transcription	Dnd41	blood
20	chr20:13504600-13516200	Weak transcription	Brain Hippocampus Middle	brain
21	chr20:13505800-13517000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr20:13506000-13517200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr20:13506400-13516800	Weak transcription	NH-A	brain
24	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr20:13506600-13514600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr20:13506600-13516000	Weak transcription	HUVEC	blood vessel
27	chr20:13506600-13517800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:13507000-13515800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr20:13507400-13514600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:13507800-13526200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr20:13508000-13517800	Weak transcription	Gastric	stomach
32	chr20:13508000-13527000	Weak transcription	NHEK	skin
33	chr20:13508000-13534000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr20:13508000-13542000	Weak transcription	Fetal Intestine Small	intestine
35	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr20:13508200-13513800	Weak transcription	Spleen	Spleen
37	chr20:13508200-13514800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr20:13508200-13525000	Weak transcription	A549	lung
39	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr20:13508400-13515600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr20:13508400-13519800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr20:13508400-13538000	Weak transcription	HepG2	liver
43	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
44	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
45	chr20:13508400-13556000	Weak transcription	HSMM	muscle
46	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr20:13508600-13516800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:13508800-13514200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr20:13509000-13527200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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