Variant report

Variant	rs2057258
Chromosome Location	chr20:13559616-13559617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1012242	0.84[YRI][hapmap]
rs13039162	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13042843	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2001178	0.86[YRI][hapmap]
rs2057259	0.82[JPT][hapmap];0.89[MKK][hapmap]
rs2070305	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2070334	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs2073324	0.84[ASN][1000 genomes]
rs2103972	0.87[ASN][1000 genomes]
rs2180569	0.82[JPT][hapmap]
rs2182708	0.84[ASN][1000 genomes]
rs2208208	0.81[ASN][1000 genomes]
rs2273480	0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs3747931	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs3789342	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3789347	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3789348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs4813131	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4814236	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4814238	0.82[ASN][1000 genomes]
rs4814242	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4814246	0.86[YRI][hapmap]
rs6042106	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs6042128	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042153	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042192	0.86[YRI][hapmap]
rs6074611	0.84[ASN][1000 genomes]
rs6074612	0.82[ASN][1000 genomes]
rs6074613	0.83[ASN][1000 genomes]
rs6074618	0.84[ASN][1000 genomes]
rs6074627	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079058	0.81[CHD][hapmap]
rs6079066	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6079072	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs6079074	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6079075	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs6079077	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs6079085	0.84[ASN][1000 genomes]
rs6079095	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs6079106	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6105096	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6105103	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs6105113	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109887	0.82[EUR][1000 genomes]
rs6109891	0.81[ASN][1000 genomes]
rs6109903	0.81[EUR][1000 genomes]
rs6109905	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6109935	0.86[YRI][hapmap]
rs6109958	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6131476	0.81[CHD][hapmap]
rs6131483	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6131485	0.84[ASN][1000 genomes]
rs6131488	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6134902	0.83[ASN][1000 genomes]
rs6134912	0.87[ASN][1000 genomes]
rs6134919	0.82[JPT][hapmap];0.89[MKK][hapmap]
rs73086013	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	esv1797514	chr20:13541011-13610424	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv912688	chr20:13546903-13589682	ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
3	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
7	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
8	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
9	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
10	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr20:13527800-13563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr20:13534600-13563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr20:13534600-13563600	Weak transcription	Lung	lung
14	chr20:13535000-13563400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr20:13535200-13560200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:13535800-13561400	Weak transcription	NHEK	skin
18	chr20:13536800-13563400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr20:13537400-13563600	Weak transcription	Placenta	Placenta
20	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr20:13539000-13560600	Weak transcription	Thymus	Thymus
22	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr20:13544200-13563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr20:13545000-13567000	Strong transcription	Dnd41	blood
25	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr20:13546400-13563400	Weak transcription	Fetal Brain Female	brain
27	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr20:13547600-13565600	Weak transcription	Osteobl	bone
29	chr20:13547800-13563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr20:13547800-13563600	Weak transcription	Fetal Kidney	kidney
31	chr20:13548000-13560600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr20:13548000-13563400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr20:13548000-13568600	Weak transcription	Brain Angular Gyrus	brain
34	chr20:13548600-13563600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:13548600-13566200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr20:13548600-13568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr20:13548600-13584600	Weak transcription	Gastric	stomach
38	chr20:13549000-13563400	Weak transcription	NH-A	brain
39	chr20:13551200-13563400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr20:13551600-13563600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:13551800-13563400	Weak transcription	Esophagus	oesophagus
42	chr20:13553000-13563400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:13554000-13568400	Weak transcription	Fetal Brain Male	brain
44	chr20:13554400-13563400	Weak transcription	Right Ventricle	heart
45	chr20:13554600-13577400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr20:13554800-13567000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr20:13555000-13563400	Weak transcription	Left Ventricle	heart
48	chr20:13555600-13560400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:13555800-13560800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr20:13556000-13560400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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