Variant report

Variant	rs6042242
Chromosome Location	chr20:13589144-13589145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1024208	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1028849	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10439586	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12329620	1.00[CEU][hapmap]
rs12479480	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12479594	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12479746	1.00[ASN][1000 genomes]
rs12480101	1.00[CEU][hapmap]
rs12480131	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480266	1.00[JPT][hapmap]
rs12480276	1.00[JPT][hapmap]
rs12480277	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12480426	1.00[ASN][1000 genomes]
rs12480587	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12481107	1.00[ASN][1000 genomes]
rs12481490	1.00[EUR][1000 genomes]
rs2145140	1.00[JPT][hapmap]
rs2180570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327755	1.00[JPT][hapmap]
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]
rs6033774	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6033782	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033784	0.93[AFR][1000 genomes]
rs6033802	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033806	1.00[EUR][1000 genomes]
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]
rs6042233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6042243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042246	0.98[AFR][1000 genomes]
rs6042247	0.91[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042248	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042249	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042252	0.98[AFR][1000 genomes]
rs6042265	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042267	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042274	1.00[ASN][1000 genomes]
rs6042275	1.00[ASN][1000 genomes]
rs6042284	1.00[ASN][1000 genomes]
rs6042307	1.00[EUR][1000 genomes]
rs60686384	1.00[ASN][1000 genomes]
rs6079117	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	1.00[ASN][1000 genomes]
rs6105146	1.00[ASN][1000 genomes]
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]
rs6109967	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109972	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109973	0.82[YRI][hapmap];0.98[AFR][1000 genomes]
rs6109985	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61518689	1.00[ASN][1000 genomes]
rs7274078	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73254604	1.00[ASN][1000 genomes]
rs73268992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73270770	1.00[EUR][1000 genomes];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:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
3	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:13564000-13602600	Weak transcription	Ovary	ovary
8	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
9	chr20:13564200-13591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr20:13564200-13592400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr20:13564200-13608400	Weak transcription	HSMM	muscle
14	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
16	chr20:13567400-13589200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr20:13567400-13594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:13567400-13597400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr20:13567400-13602800	Weak transcription	A549	lung
20	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr20:13567400-13608400	Weak transcription	HMEC	breast
23	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr20:13568800-13589200	Weak transcription	HepG2	liver
27	chr20:13568800-13602800	Weak transcription	Fetal Intestine Large	intestine
28	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr20:13574200-13606600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:13574400-13606400	Weak transcription	Thymus	Thymus
32	chr20:13574600-13606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:13577400-13590600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr20:13581000-13595800	Weak transcription	NHEK	skin
35	chr20:13581200-13606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr20:13582000-13603000	Weak transcription	Liver	Liver
37	chr20:13582200-13606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:13582600-13608000	Weak transcription	HSMMtube	muscle
39	chr20:13583200-13602800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr20:13583200-13607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:13583200-13607200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr20:13583400-13607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr20:13583600-13591400	Weak transcription	Primary T cells from cord blood	blood
44	chr20:13583800-13605400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr20:13584000-13589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
47	chr20:13584200-13594600	Weak transcription	Fetal Stomach	stomach
48	chr20:13584400-13589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr20:13585000-13589400	Strong transcription	Dnd41	blood
50	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas

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